I was able to get a sort of repro on our internal Discourse instance. Unfortunately I can’t post about it here since it has a bunch of private data in the screenshots, but I have a definite repro – and it repros even in the topic itself, that is, if you click through to the topic it looks like it has no category. Once you press the edit button on the title, then and only then do you see the category is really there!
It also persists between navigation to various topics and back to the topic list.
So, I don’t know how I got the topic to that state, other than replying to it, but it’s a very “sticky” problem that is only “fixed” by refreshing the entire page with f5.