In "Brain Candy's" case, I think it was bad timing. Lots of sketch comedy shows were coming out with feature films around this time, and most of them failed because they attempted to take something that was funny for 5 minutes at a time and transform it into a 90 minute cohesive story. Brain Candy wasn't like that at all, but a lot of people (including myself) wanted the best of both worlds, which, besides "Kentucky Fried Movie" is an impossible task.
It's not that hard to understand. It had some funny moments (like the one in this clip) but many of its jokes fell flat. And there were long stretches of the movie that didn't have any jokes or anything interesting at all.