Something is definitely wrong if you checked in at UA counter and your MP# was on reservation. If your one bag was under 50 pounds, there should have been no charge instigated by the kiosks. A note to UA's customer service w/ MileagePlus number, confirmation number, and copy of your receipts ought to do it.

I asked about United counter because people checking in, for example, at Hawaiian for a UA codeshare flight operated by Hawaiian don't get UA's Premier bag fee waiver.