Can't actually equip both of the same spell, but I feel like they aren't supposed to be there. At level 5 I had two Aid but only 1 Shield of Faith.

Also, considering how each class really doesn't get that many spells, have you considered making them larger and/or flashier looking? Like big proper spell cards or something?

I can't seem to reproduce this one. Did it occur directly after updating the mod?

Nimbus has been duplicated for me as well, this is after updating.

Does this occur still after you do a minor reset

It does indeed

Looks like any spells I already knew are copied when starting up the game, but spells learned that session are not copied until fully restarting Minecraft. Never copies spells already copied.

I had the first three spells here already, and just learned Stalwart Pact this session:

Does this issue still exist in the latest build?

It appears to be fixed.