So i took my first AS codeshare flight last week (operated by AA) and feel like I got burned!! Mileage credit on AS didn't automatically show up. A 5 min call to AS customer service took care of that!

Checked in a bag. AA counter agent at SJC tells me that I had to pay $25. Had her confirm my MVP Gold membership number back to me (it was correct). She said that her computer is telling her to collect $25 and that I would have to ask for a refund later from AA customer service.

Rather than have the situation deteriorate (over $25) I handed over my credit card.

Next week I'm flying SJC-DFW-SJC. This time booked an AA ticket (no codeshares). Have already called AA to confirm MVP Gold # is entered.

If the $25 fee comes up again is there anything I can point out to the agent to correct? or anything I can do to mitigate this when i'm at SJC AA checkin counter?

Am I missing something obvious here? Should I be asking my corporate travel (Concur/Amex Business Travel) to do something different when booking my flights?

I've never had a benefit problem when flying United partners (as UA 1K MM) so i'm trying to figure out if it's just a silly noob user error on my part as I get used to AS mileage program....