I am pretty sure that Thetrainline are charging incorrectly, and there have been stories about this before.
I've been charged twice by thetrainline, and they were not helpful at all, so I contacted my bank and got them to reverse one of the charges. Never heard anything back from thetrainline.
Confirmations with missing reference numbers have also occured, and this means they did not actually complete the booking.
For nearly a year Thetrainline refused to charge railcard discounts on PBO-YRK/DON day returns, they kept sending standard messages back such as "We are looking at the problem" when the evidence suggested otherwise.
Their customer support is well-known to be poor, with the people there to "help" you being based somewhere like India and have very little knowledge of anything. I think they work from a simple script. I was once told I could buy a SVR from KGX to YRK for about £3. (The exact background behind that is very complicated, but it's to do with the FSR50 offer and the way they calculate discounts...).
I was once given the option of a York-Newcastle ticket for 15p, but the ticket never arrived. Obviously a mistake - but theirs! Thetrainline were rubbish in dealing with it, and left it to Virgin (whose train I was booked to get) to handle it (to be fair Virgin were great!).
Their refund policy is extremely dubious, for example if you are badly delayed on an advance ticket and try to claim a refund it says "No refund allowed on that ticket type" which is FALSE. I sent my ticket to the company I travelled with and got the full amount back in vouchers.
Overall, my opinion of thetrainline is very low. I've spent a 4-figure sum on tickets through their website until now because there has been no other choice. Now, fortunately, NXEC (formerly GNER) have an alternative!
http://www.nationalexpresseastcoast.com/