This is a problem that we are actively working on. You may or may not be aware that each seat is configured to permit reservations for a range of fares. Those might be all valid fares fo the service, a election of them, or none at all. Right now we try quickly to reserve the first "available" seat in each carriage using the fare you have chosen. If we can book it we assume that this coach is ok for your fares and offer you all the seats that NRS says are available in it. If it doesn't then we assume that none of other seats wil either and exclude that coach.
This works ok on some services but really doesn't for other - the one you tried being one of them.
We are busy working on a major update that will provide you with accurate availability for your chosen fare in every seat, not just checking one seats an extrapolating out to the whole coach. I do not have a release date for this update yet, and when I do, TrainSplit will need to makes some changes to use our new function. But we will get this rolled out as quickly as possible. In the mean time, please bear with us where there are these problems...