I had a similiar problem – all of my categories were appearing the upper left-hand corner of the page.
I know very little about the upgrading process, but I started deactivating all of my plugins (one at a time) until the problem went away.
I had one plugin to create a category cloud (where the text appears larger, according to the number of posts).
https://zak.greant.com/catcloud
Once I updated this plugin everything was fixed.
I’m sorry I can’t help with the technical problems, but this might be one process to try and determine where the problem is coming from. Good luck!
