It’s happening to mee too!
The problem is what you fill in first categories block, will be rewritten by what its filled in second categories block. that’s terrible.
I wasnt understanding how all caterogies Ive filles was substituted by “no-category” option. Nothing was making sense. Until I saw this second block of categories there in editor of 5.0.
And the problem is: the first one is easy to find the category you want, typing the inicials, the second one, does not permit it, so, its hard to check boxes when you have more than hundreds os options (section, source, theme, subject, and others classifications).
Ive tried to remove plugins to blame them (like elementor) and nothing changed until I see this thread of discution.