TL;DR remove all your spells from your spell slots before you retrain, or you might end up with a bugged UI for the rest of the game on that save file.

Long version: I've encountered this bug so far with two characters, namely the Fatebinder and Verse, so I assume this bug will likely happen to any other characters too. Basically, your spell menu will end up with a "ghost" spell that cannot be removed, and will also prevent the new spell in the "ghost" spell's slot to not appear. Given that I was on POTD...things did get hairy now and then because of it...

As far as I've observed, once saved, this bug persists, and cannot be removed with restarting your game. So keep lots of saves in case you need to roll back. The best way to prevent this seems to be removing all spells from their slots before you retrain.

As to how this bug came about, I'm not sure if it is caused by retraining while you have spells in those spell slots, or retraining in such a way that you end up with a different number of spell slots than you had before. If anyone else can give a bit of input, it'll be greatly appreciated!