This is a bug on PS5 at the very least, though I have not tested for Xbox or PC versions of the game.
I have also only tested this with the spell "Thunderwave", by learning it through levels in Wizard and also levels in Storm Sorcerer and Tempest Cleric, where it is always prepared.
Intended behavior:
If Thunderwave is learned multiple times through levels in different classes classes, different versions of the spell should be able to be selected and used so that the player can choose which spellcasting modifier to utilize. If the spell is learned through all three Wizard, Sorcerer, and Cleric levels, the player should have access to an INT scaling Thunderwave from Wizard, CHA scaling Thunderwave from Sorcerer, and WIS scaling Thunderwave from Cleric. In most cases, this is how learning a spell from multiple different classes works.
Description of the bug:
When Thunderwave is learned and prepared from levels of Wizard, and also learned and prepared from levels of Storm Sorcerer or Tempest Cleric (both subclasses where the spell comes "always prepared"), the player ONLY has access to the "always prepared" version of the spell, and the INT scaling Wizard variation disappears from the Wizard's learned spells altogether and cannot be selected by the player for preparation or use.
Impact on Gameplay:
When multi-classing as an INT-forward spellcaster, learning Thunderwave from other classes, if it comes always prepared, limits the effectiveness of the spell because it forces the player to use a version of the spell that scales with a lesser ability modifier.
