The way she entered into the booking must have changed the whole booking. Always a dangerous thing to do personally speaking. I would have put the A3 number into the booking and then taken it out for the GVA LH sector then do a retro claim with M&M . You would have been better to have nothing in then risk it going to the wrong program which as it turns out has credited everything to the wrong program.
You cant do a retro claim now on A3 as its already credited to your M&M account. Sadly there is no going back .
Your only course of action would be to email M&M and explain it but Im not hopeful.