The most obnoxious example I recall offhand is the Aardwolf maze, but I'm sure there are others, especially in retail expansions. (For a fan mod, one can in principle report the bug, or patch it and redistribute.) I suppose you'd auto-detect the WAD similarly to how ZDoom auto-detects certain maps to force a particular compatibility level.
Last post from me, Blzut3 -- I swear I had listed five or ten more bugs with some meat on them, but then I couldn't reproduce, or had remembered the vanilla behavior wrong. :D