Count it as a small mercy and shut up! (in the nicest possible sense). If you have your evidence of bookings, PNRs etc, I wouldnt question it any further. I would frequetly check the status of the booking online though, to ensure it doesnt disapear. It would be very unlikely for it to do so, without someone from Revenue calling to clear up a small discrepency at their end.... Surely?

I had this once when I bought a very high-spec laptop costing £2k. I paid a £100 deposit by phone, and then went to the store the following day to buy the laptop and take it home... I paid the £1,900, got a receipt, and walked out with my purchase. 4 years later and it has still never come up on my credit card bill. I certainly wasn't going to call the credit card company in question to query it!