So I decided to try a custom companion and went to bar to hire one.
I make a mage and remove Aloth from the party.
As I go over my new mage to adjust her grimoire, I notice that all 1st level spells are unassigned (no written spells). So I click on them to assign them, nothing happens. 2nd and 3rd level spells work fine.
I go back to the castle and bring in Aloth. Then notice that 3 grimoires he had in his quickslots are gone. They aren't in the stash either.
I drop another character and bring in the new mage again and give her Aloth grimoire and scribe/learn a few spells from him.
I go in to adjust again, now 1st level spells work properly and I can assign them, but 2nd level spells don't. The only spell I could put in was Necrotic Lance. Clicking on others does nothing again.
Very weird