XCOM 2 code is broken into chunks called "classes". One of the main ways to mod XCOM 2 is to override these classes to force custom code to run instead.

Unfortunately, only one mod can override a given class. If two mods attempt to override the same class, one of those mods will have their changes thrown out. Depending on the mod, this could cause small bugs, or it could cause the game to crash completely.

Your only options as a user are to change the mod load order, or disable one of the conflicting mods.

The load order can be seen in
Unfortunately, editing this file does not work; Steam overwrites it. The only way I've found to actually change the load order is to unsubscribe from all mods, and resubscribe to them in the order you want them loaded.

If two mods attempt to override the same class, whichever mod loads last wins. For some mods, having some code not load is fine. For others, it's catastrophic.

For example, Stop Wasting My Time removes a 2.75 pause by overriding the class "X2Action_EnterCover". Let's say a mod called Cover Reworked also overrides that class. If Stop Wasting My Time is loaded first, then Cover Reworked takes precedence and the 2.75 pause returns. However, if Cover Reworked is loaded first, Stop Wasting My Time takes precedence and Cover Reworked breaks, maybe crashing the game.

None of the changes in Stop Wasting My Time are essential. For this reason, it's recommended that you always load 'Stop Wasting My Time' first!

I've updated all my mods to include that information in the description. For other mods, you'll have to dig through their source-code. The only reliable method is to find the mod under
then open Config/XComEngine.ini, and search for lines beginning with +ModClassOverrides

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The mod launcher is broken, disabling a mod from there doesn't always work. The most reliable method is to unsubscribe from the mod in the Steam workshop.

When a mod makes changes to the configuration files, sometimes these changes get permanently saved to disk. For example, many users have complained that the 10% increased movement speed in Stop Wasting My Time persists after uninstalling the mod.

Unfortunately this seems to be a bug in XCOM 2, and there's nothing we mod creators can do about it. The only workaround I'm aware of is to go to
and delete all the files there. This will remove all your game settings, including graphics settings and custom key bindings. It does not delete your save files or your list of Steam Workshop subscriptions.

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When you subscribe to a mod, Steam downloads it using the same process it uses to update and install games. If you have another game installing or updating, or your installs/updates are not downloading for any other reason, you will not get mods installed.

In 99% of the cases, doing one of these two things will fix it:

• In Steam, go to Library --> Downloads. Find "XCOM 2 - Workshop Content", and click the 'up' arrow on the right.
  
• Restart Steam

I've also heard of people having success deleting the config files (see previous question), though I'm not sure why.