Oh, I misread the OP. I thought it was a r/t and they got the 3 bags on the outbound. In that case, then I have no idea why it printed Premier Access on the BPs, though likely a glitch owing to the 1K GPUs applied. And since they were purchased on May 29, my other answer of purchased before the baggage change also doesn't apply.
So all I can say is that they should've gotten 1 free bag because the upgrade hadn't cleared, and if they did you a favor of a 2nd free bag, that says nothing about the 3rd bag, which is indeed $200. If the favor was to give the C allowance, then they screwed up.
And all should be moot if you have the domestic F anyways. File for a refund, and only if that fails dispute the charge.