The affinity in my pack is pretty low and the main issue seems to be my alpha. None of my other wolves, apart from his mate, like him. Is there a way to fix this?

Not really, other than selling/retiring him

You can buy an item called "Make Friends" at Realm > Barter > Apples. That will make his affinity excellent.

Some wolves are very picky over who is in there pack some of them do great with their pack while others don't