I got confused at this as well, Clara specifically said she seen all eleven of his faces as if that's all that was there. Also the tomb was Matt Smith's TARDIS interior as well. I can kind of justify it to myself by saying that as the future is still in flux and changes depending on today's actions the GI didn't need to attack it, as long as he took out everything from before that day the future wouldn't exist anyway. So Clara only went for the stuff under attack. Under this theory though all he had to do was go after William Hartnell's timestream.
The other theory I had on this was at the time she entered his timestream there was no future Doctors, Matt's Doctor was just about to enter it himself, he should be dead with no regeneration so there wouldn't be future Doctor's. This also ties in with the paradox of him being there he brought up. Would there be a timestream of his life in the first place if he died inside it and he was scattered as echoes through time? For him to have a timestream he needs to die, but for him to die he needs to access his timestream. My brain hurts.