1 - Follower weight limit - If I remove an item from the follower's inventory and then try to replace the same item, I get the "item too heavy" error message. So, recharging an enchanted item for them is a problem

2 - Bookshelves - Shelves that were broken before the patch are still broken.

Otherwise, I be having a good day in Skyrim.

#2 is known - they said that if they were broken they're going to stay broken, at least in 1.3.

#1, I'm going to guess that the difference is that they had it equipped so it wasn't counting toward their carry limit. You took it away, and trying to put it back would put them over their limit.