So I have this mage follower I made and he works fine, I can get him to follow me and he uses his spells that I have assigned him. However For some reason he has these bow and arrows equipped. He is a new NPC I made and he has nothing in his inventory. Anyway to fix this? Does he just default to a bow because he has nothing in his inventory? When I actually speak to him in game and tell him to carry something his inventory there is also empty so I have no idea.

The follower reference alias automatically gives them a bow and arrows. You can probably write a script to remove them for that specific NPC, or go into the FollowerDialogue quest and edit the reference alias so it doesn't give out those items. The latter method will affect all followers though.