I've always had a problem with the way BB handles this. They need to go back and retroactively bot all the games they've played in.
On the one hand, I agree with you that it seems unfair for some people to get a free one and other to not.
On the other hand, in a case like this, where the team went bot almost immediately after starting the inter-conference games, I feel like the most fair thing to do is leave it alone. Otherwise everybody in one conference will get two free wins and everybody in the other conference gets only one.