I agree with you. There were some of us, including myself , who thought we did look fitter in pre season though, and were pleased to hear RM talk about “ run harder” etc and that he was aware of the concerns about fitness .
Youngsters should be able to run all day- I remember myself at 21 in local football; 3 games in a weekend😂! So you’re right, seeing the academy players in the friendlies sprinting and showing bags of energy gave us false hope.
I wonder if the approach of careful passing and low risk systems sets a sub conscious tempo for some players, which they find out to shake out of in the latter stages of a game.