Replication steps:

1. Obtain a yoyo

2. Add the collecting enchantment using an anvil

3. Toss a handful of enchanted books on the ground in one place

4. Use the yoyo to pick up the books

What I expect to happen: Each enchanted book will enter my inventory as a different item stack

What actually happens: The enchanted books will stack

I was able to replicate this with the enchantment and Tinkers' modifier. It also affects enchanted diamond swords, white shulker boxes with different contents, and beds. However, it did not stack blue and white shulker boxes (different block IDs), white and blue carpets (stackable), or white and blue beds (different meta data values).

It would appear that for the bug to occur, the following conditions must be met:

-The items must be unstackable
-The items must share a block ID
-The item must share a meta data value

The NBT data doesn't matter. When they stack, the NBT data of all of the items will be overwritten except one.

Fixed in abaca16

It was because I wasn't respecting the items' max stack size.