These things are pretty obvious, but they've happened to me in the past.
Direct mic obstuctions...
seems to happen mostly when running stage-lip, on-stage, or mics at head-height. Mics that are blocked in some way (heads, hands, bodies) from a PA or an Amp on stage etc. for a brief time can muffle the recording. I've had people actually put their hand in front of them, take off the wind screen, fiddle with them and what not. If you saw a cell phone sitting next to someone... would you pick it up and start fiddling w/ it? Sorry, just venting...hahaha.
wind...
can be a big annoyance it "flutters"(for lack of a better word) the high end or you hear wind "whooshing" noise. Sometimes windscreens just won't help. Also, I've had huge gusts of wind blow my mic placement off which resulted in some audable wierdness on the recording. Kinda sucked, I guess the stand thumb screws weren't tight enough. Hahaha, end user error I suppose.
Rain...
can be an annoyance as well... I've heard umbrellas flap and rain drop noise on recordings. Again, not much you can you do about it.
-K