For Oblivion, I created a rather large quest mod called "Path of the Skull Bearer." There is a certain part where you have to collect a gem. You are lead to a "mausoleum" thing, and click on it, and some burning creatures appear.
The creatures are made to be impossible to kill (not even taking damage, not merely essential) with scripts (things like resethealth on hit if I remember correctly.) You are meant to "forgive" them, and it is very obvious in the quest that this is what you are supposed to do (http://youtu.be/e__tV_nRapQ?t=6m44s note the voiceover). I got emails weekly for a time, that they killed the monsters but nothing happen. "Oh, how did you kill them? They are not supposed to take any damage." "I used the console kill command, your mod is broken, please fix."
I have not had anything quite so bad occur with Skyrim yet because I haven't released any large mods, but I know it is going to happen.
I'm sorry for ranting, but this has to be my number one complaint about mod users. It is not reasonable to think that using console commands to cheat (especially to "cheat wrongly" as above) will just be 100% compatible with the scripted progression of the mod.