Wife and I flying BOS-LAX tonight. Originally on 1 PNR, but was split into 2 solely because of how the agent processed the payment (used a voucher). Agent at booking ensured the upgrade priority would be linked and processed together - note in PNR states that clearly.

Sure enough, my upgrade (Plat) processed ~5 hours out, and hers (Gold) didn't - and now F is full. My questions:
1) How much hell should I raise? My instinct is that, unless I was the last upgrade (seats for sale went from 6 to 1 instantly), they upgraded someone else inappropriately over my wife. What are my immediate options?
2) What compensation, if any, should I ask? I realize one of us got upgraded to First, so there are worse things in life...but this is just flat-out incorrect.

Thanks!