Okay, I did some further digging. I compared the migration files from Xibo 2.0.1 to the migration files from 2.0.0 and they’re the same, so the database is not the cause of the error.
Next I tried following the link in the error message. I did the steps described in the Diagnosis section and found what is causing the error message (layouts, logs etc). Every time Xibo makes an Ajax request on one of the pages where I get error messages, it receives an HTML file with a 404 error code instead of the JSON it is supposed to receive.
However, I don’t know what the cause for the 404 error is and I don’t think I can figure this one out by myself. Any help with this error is appreciated.
Edit: nevermind, I figured it out after doing a Google search with regarding Ajax and Xibo upgrade. This solved it: Ajax request fails after 1.8.2 upgrade