Structural ones, mainly. One was among the coolest things I've ever FREDded, a sneaking mission over a moon. But once the sneaking was done, the rest of the mission just didn't work. It was awkward to play and not fun, and I couldn't figure out how to make it fun. Another was too short, but extending it kind if made it make no sense: I think I basically need to make a new mission to extend it.
Also, I recall the last time I played through there were balance issues that I dont recall being there previously, and might represent changes in the way the game plays over the years.
Really, none of these should have been showstoppers, but it's somehow different than with technical bugs. There's no obvious endpoint, I guess.