Not game-breaking, but really weird:
I like to merge mods, so I pull things from a mod and then disable that part in the source by adding a // in mod.txt or parts.txt
In the Star Wars ACD mod there is a weapon called blue_blasterlaser which I disabled long ago. Then after working on a completely unrelated part in a totally different mod, I receive an error that this laser failed to load... I go to the SW mod.txt - and the // is gone
First time I thought that was just me, even though I didn't have a problem with the laser failing before.
A day after it happened again - same blue_blasterlaser unlocked itself, even though I didn't even touch the mod.txt