Hi PaQ, can you possibly send me that model so I can repeat the problem over here?

It looks like you probably got a "disjoint brep" in that situation there, which is a brep made up of more than one boundary skin but still defines a solid volume in separate pockets.

I would guess that if you save that to a file and re-open it that it will end up broken up into different pieces like you would more expect.

Normally there are some volume separation type steps for commands that could otherwise easily create this kind of a thing such as Join or booleans, it looks like I need to add that processing to filleting as well.

So really that looks like a tuneup needed for Fillet actually. If you can possibly send me the pre-filleted shape over here so I can repeat the Fillet and see the problem happen that would make it easier for me to fix it up.

- Michael