So here's a weird bug:
it seems that sometimes for some reason a colonist will put the nutrient and the protein in a cloning vat but forget the genome. The sprite of the cloning vat will not show a growing clone and extracting the clone will just clear the "growing" status but not create anything.
The genome assigned to the vat will remain in storage after the cloning process begins, confirming that it has indeed been omitted.

This results in the game no longer considering cloning vats to be cloning vats and they suddenly all become useless, the "grow clone" option becomes "grow organ" but doesn't work at all.
It appears to corrupt clone vats functionality for the entire save from that point on.

No clue how to reproduce the pawns not putting the genome in the vat but testing on a different save did show that the cloning works as long as this doesn't happen.



Looking at the save file, the broken vat looks like this:

<thing Class="QEthics.Building_PawnVatGrower">
<def>QE_PawnVat</def>
<id>QE_PawnVat1959662</id>
<map>0</map>
<pos>(179, 0, 141)</pos>
<rot>1</rot>
<health>1000</health>
<faction>Faction_31</faction>
<parentThing>Thing_PowerConduit413519</parentThing>
<glowOn>True</glowOn>
<craftingProgress>1320000</craftingProgress>
<status>Finished</status>
<innerContainer Class="Verse.ThingOwner`1[Verse.Thing]">
<innerList />
</innerContainer>
<orderProcessor>
<desiredThings />
</orderProcessor>
<pawnKindToGrow>Colonist</pawnKindToGrow>
<scientistMaintenance>0.6447106</scientistMaintenance>
<doctorMaintenance>0.6265738</doctorMaintenance>
<pawnBeingGrown IsNull="True" />
</thing>

error log when opening the vat:

JobDriver threw exception in initAction for pawn Saio driver=JobDriver_ExtractGrowerProduct (toilIndex=3) driver.job=(QE_ExtractFromGrowerJob (Job_9776207) A=Thing_QE_PawnVat1959662) lastJobGiver=Verse.AI.ThinkNode_QueuedJob
System.NullReferenceException: Object reference not set to an instance of an object
at QEthics.Building_PawnVatGrower.ExtractProduct (Verse.Pawn pawn) [0x00000] in <filename unknown>:0
at QEthics.JobDriver_ExtractGrowerProduct.<MakeNewToils>b__1_0 () [0x00000] in <filename unknown>:0
at Verse.AI.JobDriver.TryActuallyStartNextToil () [0x00000] in <filename unknown>:0
Verse.Log:Error(String, Boolean)
Verse.AI.JobUtility:TryStartErrorRecoverJob(Pawn, String, Exception, JobDriver)
Verse.AI.JobDriver:TryActuallyStartNextToil()
Verse.AI.JobDriver:ReadyForNextToil()
Verse.AI.JobDriver:DriverTick_Patch1(Object)
Verse.AI.Pawn_JobTracker:JobTrackerTick()
Verse.Pawn:Tick_Patch1(Object)
Verse.TickList:Tick()
Verse.TickManager:DoSingleTick()
Verse.TickManager:TickManagerUpdate()
Verse.Game:UpdatePlay()
Verse.Root_Play:Update()

error log when clicking on the grow button on a broken vat:

System.NullReferenceException: Object reference not set to an instance of an object
at QEthics.Building_PawnVatGrower.<GetGizmos>b__35_0 () <0x003d0>
at Verse.Command_Action.ProcessInput (UnityEngine.Event) <0x0002c>
at Verse.GizmoGridDrawer.DrawGizmoGrid (System.Collections.Generic.IEnumerable`1<Verse.Gizmo>,single,Verse.Gizmo&) <0x00bb6>
at (wrapper dynamic-method) RimWorld.InspectGizmoGrid.DrawInspectGizmoGridFor_Patch0 (System.Collections.Generic.IEnumerable`1<object>,Verse.Gizmo&) <0x00702>

Verse.Log:Error(String, Boolean)
Verse.Log:ErrorOnce(String, Int32, Boolean)
RimWorld.InspectGizmoGrid:DrawInspectGizmoGridFor_Patch0(IEnumerable`1, Gizmo&)
RimWorld.MainTabWindow_Inspect:DrawInspectGizmos()
RimWorld.InspectPaneUtility:ExtraOnGUI(IInspectPane)
RimWorld.MainTabWindow_Inspect:ExtraOnGUI_Patch1(Object)
Verse.WindowStack:WindowStackOnGUI()
RimWorld.UIRoot_Play:UIRootOnGUI()
Verse.Root:OnGUI()