Something slightly similar happened to me just over a year ago. From memory I think what happened was this. I upgraded a group of 3 from ET to CE on an LGW flight. The E ticket receipt showed about 3 times the amount I was quoted on BA.com. The initial charge to my card was the amount shown on BA.com, but the balance between that amount and the amount shown on the E ticket receipt was debited from my card a few days later.

I didn't make a fuss, because the initial amount quoted on BA.com was surprisingly low (and was almost certainly a mistake), and I had already told the friends I was travelling with that I had done a cheap online upgrade. I didn't want to end up arguing with BA, get put back in ET and disappoint them. But I was a bit annoyed, and I've avoided post-booking upgrades on BA.com since then.