Mods listed below have issues during world gen. All testing is done on Large-size worlds with random seeds and random evil selected. Classic difficulty.
Testing for these issues are replicable and in no way meant to showcase faults with development in a negative light. With no other mod enabled aside from dependencies for each given mod, each has been tested many many times to test for all possibilities that can be encountered during worldgen.

With Origins enabled

1st fail (15% error w/o crash)

[06:30:56.250] [Main Thread/INFO] [tML]: Expanding infrastructure...
[06:30:59.014] [.NET TP Worker/WARN] [tML]: Silently Caught Exception:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at Remnants.Content.World.StructureTools.GenericLoot(Int32 chestIndex, List`1 itemsToAdd, Int32 grade, Int32[] uniquePotions, Boolean haveRestorationPotions) in Remnants\Content\World\General.cs:line 929
at Remnants.Content.World.Microdungeons.ApplyPass(GenerationProgress progress, GameConfiguration configuration) in Remnants\Content\World\Structures.cs:line 4254
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
at Terraria.WorldGen.GenerateWorld_RunTasksAndFinish(Int32 seed, Stopwatch generationStopwatch, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 14056
at DMD<DMD<>?13366967::Terraria.WorldGen::GenerateWorld>(Int32 seed, GenerationProgress customProgressObject)
at SyncProxy<System.Void Terraria.WorldGen:GenerateWorld(System.Int32, Terraria.WorldBuilding.GenerationProgress)>(Int32 , GenerationProgress )
at Terraria.WorldGen.do_worldGenCallBack(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2508
at Terraria.WorldGen.worldGenCallback(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2497
at System.Threading.ExecutionContext.RunFromThreadPoolDispatchLoop(Thread threadPoolThread, ExecutionContext executionContext, ContextCallback callback, Object state)
at System.Threading.Tasks.Task.ExecuteWithThreadLocal(Task& currentTaskSlot, Thread threadPoolThread)
at System.Threading.ThreadPoolWorkQueue.Dispatch()
at System.Threading.PortableThreadPool.WorkerThread.WorkerThreadStart()

[06:30:59.015] [.NET TP Worker/ERROR] [tML]: A problem was encountered during world generation
[R] Microdungeons
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at Remnants.Content.World.StructureTools.GenericLoot(Int32 chestIndex, List`1 itemsToAdd, Int32 grade, Int32[] uniquePotions, Boolean haveRestorationPotions) in Remnants\Content\World\General.cs:line 929
at Remnants.Content.World.Microdungeons.ApplyPass(GenerationProgress progress, GameConfiguration configuration) in Remnants\Content\World\Structures.cs:line 4254
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
[06:30:59.015] [.NET TP Worker/ERROR] [tML]: A problem was encountered during world generation
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at Remnants.Content.World.StructureTools.GenericLoot(Int32 chestIndex, List`1 itemsToAdd, Int32 grade, Int32[] uniquePotions, Boolean haveRestorationPotions) in Remnants\Content\World\General.cs:line 929
at Remnants.Content.World.Microdungeons.ApplyPass(GenerationProgress progress, GameConfiguration configuration) in Remnants\Content\World\Structures.cs:line 4254
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
at Terraria.WorldGen.GenerateWorld_RunTasksAndFinish(Int32 seed, Stopwatch generationStopwatch, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 14056
at DMD<DMD<>?13366967::Terraria.WorldGen::GenerateWorld>(Int32 seed, GenerationProgress customProgressObject)
at SyncProxy<System.Void Terraria.WorldGen:GenerateWorld(System.Int32, Terraria.WorldBuilding.GenerationProgress)>(Int32 , GenerationProgress )
at Terraria.WorldGen.do_worldGenCallBack(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2508
at Terraria.WorldGen.worldGenCallback(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2497
[06:31:16.767] [Main Thread/DEBUG] [tML]: Process.Start (UseShellExecute = True): "tModLoader-Logs"

2nd fail (75% error w/o crash)

[06:40:49.560] [.NET TP Worker/INFO] [Origins]: Fiberglass Undergrowth
[06:40:49.560] [.NET TP Worker/ERROR] [tML]: A problem was encountered during world generation
Fiberglass Undergrowth
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at Origins.OriginSystem.<>c__DisplayClass90_0.<ModifyWorldGenTasks>b__2(GenerationProgress progress, GameConfiguration __) in Origins\World\BiomeGen.cs:line 92
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
[06:40:49.561] [.NET TP Worker/WARN] [tML]: Silently Caught Exception:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
at Terraria.WorldGen.GenerateWorld_RunTasksAndFinish(Int32 seed, Stopwatch generationStopwatch, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 14056
at DMD<DMD<>?13366967::Terraria.WorldGen::GenerateWorld>(Int32 seed, GenerationProgress customProgressObject)
at SyncProxy<System.Void Terraria.WorldGen:GenerateWorld(System.Int32, Terraria.WorldBuilding.GenerationProgress)>(Int32 , GenerationProgress )
at Terraria.WorldGen.do_worldGenCallBack(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2508
at Terraria.WorldGen.worldGenCallback(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2497
at System.Threading.ExecutionContext.RunFromThreadPoolDispatchLoop(Thread threadPoolThread, ExecutionContext executionContext, ContextCallback callback, Object state)
at System.Threading.Tasks.Task.ExecuteWithThreadLocal(Task& currentTaskSlot, Thread threadPoolThread)
at System.Threading.ThreadPoolWorkQueue.Dispatch()
at System.Threading.PortableThreadPool.WorkerThread.WorkerThreadStart()

[06:40:49.562] [.NET TP Worker/ERROR] [tML]: A problem was encountered during world generation
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at Origins.OriginSystem.<>c__DisplayClass90_0.<ModifyWorldGenTasks>b__2(GenerationProgress progress, GameConfiguration __) in Origins\World\BiomeGen.cs:line 92
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
at Terraria.WorldGen.GenerateWorld_RunTasksAndFinish(Int32 seed, Stopwatch generationStopwatch, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 14056
at DMD<DMD<>?13366967::Terraria.WorldGen::GenerateWorld>(Int32 seed, GenerationProgress customProgressObject)
at SyncProxy<System.Void Terraria.WorldGen:GenerateWorld(System.Int32, Terraria.WorldBuilding.GenerationProgress)>(Int32 , GenerationProgress )
at Terraria.WorldGen.do_worldGenCallBack(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2508
at Terraria.WorldGen.worldGenCallback(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2497
[06:40:54.277] [Main Thread/DEBUG] [tML]: Process.Start (UseShellExecute = True): "tModLoader-Logs"

Concludes usual issues with Origins (100% will fail without crash)

With Spooky Mod enabled

1st fail (80%)

-Full crash without error at "Growing the spider grotto"-

2nd fail (5%)

-Infinite hang at random step("Cultivating arcane flora" and "Performing ungodly rituals" observed so far) requiring force-close with no error-

Concludes usual issues with Spooky Mod (15% chance to generate world successfully)

With Infernum Mode enabled

1st fail (70%)

-Full crash without error at "Constructing a temple for an ancient goddess"-

Concludes usual issue with Infernum Mode (30% chance to generate world successfully)

With Secrets of the Shadows enabled

1st fail (80% error w/o crash)
[08:36:45.609] [.NET TP Worker/WARN] [tML]: Silently Caught Exception:
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.KillLine(Int32 x, Int32 y, Int32 dirX, Int32 dirY) in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 1079
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.CleanUp(Int32 left, Int32 right, Int32 top, Int32 bottom, Int32 pass) in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 1007
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.GenerateSanctuary() in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 690
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
at Terraria.WorldGen.GenerateWorld_RunTasksAndFinish(Int32 seed, Stopwatch generationStopwatch, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 14056
at Terraria.WorldGen.GenerateWorld(Int32 seed, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 6267
at Terraria.WorldGen.do_worldGenCallBack(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2508
at Terraria.WorldGen.worldGenCallback(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2497
at System.Threading.ExecutionContext.RunFromThreadPoolDispatchLoop(Thread threadPoolThread, ExecutionContext executionContext, ContextCallback callback, Object state)
at System.Threading.Tasks.Task.ExecuteWithThreadLocal(Task& currentTaskSlot, Thread threadPoolThread)
at System.Threading.ThreadPoolWorkQueue.Dispatch()
at System.Threading.PortableThreadPool.WorkerThread.WorkerThreadStart()

[08:36:45.609] [.NET TP Worker/ERROR] [tML]: A problem was encountered during world generation
SOTS: Sanctuary
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.KillLine(Int32 x, Int32 y, Int32 dirX, Int32 dirY) in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 1079
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.CleanUp(Int32 left, Int32 right, Int32 top, Int32 bottom, Int32 pass) in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 1007
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.GenerateSanctuary() in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 690
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
[08:36:45.609] [.NET TP Worker/ERROR] [tML]: A problem was encountered during world generation
System.IndexOutOfRangeException: Index was outside the bounds of the array.
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.KillLine(Int32 x, Int32 y, Int32 dirX, Int32 dirY) in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 1079
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.CleanUp(Int32 left, Int32 right, Int32 top, Int32 bottom, Int32 pass) in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 1007
at SOTS.WorldgenHelpers.SanctuaryWorldgenHelper.GenerateSanctuary() in SOTS\WorldgenHelpers\SanctuaryWorldgenHelper.cs:line 690
at Terraria.WorldBuilding.WorldGenerator.GenerateWorld(GenerationProgress progress) in tModLoader\Terraria\WorldBuilding\WorldGenerator.cs:line 51
at Terraria.WorldGen.GenerateWorld_RunTasksAndFinish(Int32 seed, Stopwatch generationStopwatch, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 14056
at Terraria.WorldGen.GenerateWorld(Int32 seed, GenerationProgress customProgressObject) in tModLoader\Terraria\WorldGen.cs:line 6267
at Terraria.WorldGen.do_worldGenCallBack(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2508
at Terraria.WorldGen.worldGenCallback(Object threadContext) in tModLoader\Terraria\WorldGen.cs:line 2497
[08:39:06.521] [Main Thread/DEBUG] [tML]: Process.Start (UseShellExecute = True): "tModLoader-Logs"

Concludes usual issue with Secrets of the Shadows (20% chance to generate world successfully)

So far, that's Origins with it's Fiberglass Undergrowth failing to generate. Information can be found here[tyfyter.github.io].

Spooky mod fails often when generating the Spider Grotto biome. Information on that can be found here[terrariamods.wiki.gg].

With Infernum Mode failing at generating the temple for an ancient goddess, I believe it's referencing The Profaned Garden. Information can be found here[infernummod.wiki.gg].

Secrets of the Shadows fails at generating it's new Sanctuary. As their wiki remains unfinished at this moment, I couldn't find any information on it anywhere. Even the Discord seems a bit vague on it's placement or design.