I noticed when I shutdown Krita on Windows I see every popup palette I opened during the session after the picture I'm working on goes away. Not sure if this is a bug or if it's even an issue. I'm running version Krtia X64 2.9.1 Git 60518b7. It doesn't really bother me but I was wondering if it's normal. I tried it on ubuntu and didn't see it but my ubuntu install is 2.8.1.

That's probably a bug in the graphics driver. It won't happen if you disable opengl, but I've seen it happen with some intel drivers and some nvidia driver versions.