Basically any example models for any of the problems you are talking about would really help to explain what you were running into in that particular case.

There are so many different possible ways that a model can be messy that it's not easy for me to 100% identify what particular issue you ran into just by those general descriptions...

Filleting involves a sequence of several pretty difficult calculations, stuff like generating surface offsets, intersecting those offsets, building fillet surfaces, extending and intersecting fillet surfaces, and constructing corner patches where several fillet pieces collide together. Each one of those stages can be sensitive to certain kinds of things.

- Michael