I used make friends on my pup. It said excellent and then as I got more wolves she went down to good. I've never had this happen. Is this a bug or has it always been like this?

Not a bug.

This has always been possible because make friends only counts towards wolves you have when the item is used. If you buy wolves afterwards, that aren't excellent to the wolf the item was used on, then that wolf's overall pack affinity can decrease due to the new wolves.
This can also be true for a wolf's overall affinity increasing from okay to good(as an example) if you get new wolves that are excellent to that specific wolf