I have identified the bug in question it is to do with a tool I used and the tool dev and myself are looking into it right now. It's not a gamebreaking bug (though it blocks you from getting the Diploma) and the gltiched out stuff only happens sometimes. Just save before using the Pokedex, and you can play as normal in the current version. It will be fixed within the next week in the next update.
To summarize:
- The bug is in the game's side, not the save's side.
- Your save will work in the next update.
- Nothing I know of will be lost by continuing to play as it is now.
- Just save before looking at the Pokedex until v4.0.3 is out.