Actually they do. Bethesda does not design the mods and therefore does not have any jurisdiction over them. Therefore crashes can and will be caused by the mods since Bethesda, obviously, didn't know what the mods would be.
Search "reference bug" and you can see how major bugs can also be introduced by "Official" stuff.
Mods will only cause more CTD if, 1.you downloaded a poorly coded mod with bugs(last I check you can crash with stock game and there are also lots of bugs in the stock game) 2.you installed too many mods(the game engine can't utilize more than 2G of ram) 3.two mods are conflicting each other in a serious manner(can also happen with multiple DLCs, but less often because DLCs are made by one entity, while mods are made by different people)
For 1, game and mods both receive patches, just download the latest version of the mod like you do with the game. If you can tolerate all those bugs in the original game, I don't see why you can't tolerate them in mods. Remember, you paid 60 bucks for the game, while all the mods came at free.
For 2, not much we players can do with the engine limitations(it's a 2006 engine), try the player made 4G exe.
For 3, learn what mods can be installed together and what cannot. Just like you won't install Nvidia Forceware and ATI catalyst at the same time right?