I've found the root of both of these issues, they are pretty easy fixes. The former is because it's trying to track events as part of a news story that doesn't exist (this isn't an issue during police raids, which do get news stories), the latter seems to have been an issue with combat paralysis in general but it happens so rarely that I guess nobody ever noticed it before.
Speaking of the first issue, it would be nice if you could also raid your own safehouse "for trouble" just so I don't have to wait for the CCS/mercenaries/the intelligence to raid my own safehouse so I can repaint its walls (kind of like what you can already do with the safehouses you can steal from the CCS)