I've just managed to have a look at this thread. Its a shame London Midland have not said which company they have passed it onto... I assume it is Virgin. It implies to me that they have not read the complaint correctly, that it is the fact the booking office at Milton Keynes Central (which is managed by London Midland) charged the customer for the honest mistake.
I would therefore take this up with London Midland again, personally I would contact them by telephone and explain the oversight and ask them to look at the matteter again.
Looking at the Oyster journey history, it sounds like the card had been charged for 2 incompleate journeys 17.04 and 19.13 (the ones with "no touch in" and "no touch out") both on 12 May 2015. Have you contated Transport for London to have this adjusted and the correct amount charged. I hear that TfL are very good on thigs like that. I would certainly explain the circumstances to them.
Have you heard back from Virgin Trains yet?
Hi, LM say they have passed to Virgin but I have already written to them, have a case number and await a formal response.
Thanks for the TFL advice - thought that might have to be repaid by one of the operators concerned?