The Three Lions put in a stodgy and slow display against their group rivals at Wembley, with captain Harry Kane struggling to make an impact and being starved of service.
Neville, the former England coach, criticised full-backs Luke Shaw and Reece James - both brought into the side by Gareth Southgate having sat out the first game - for not providing an attacking threat.
England struggled to create chances despite having Mason Mount, Phil Foden and Raheem Sterling on the pitch, while Jack Grealish was introduced in the second half, and Neville feels they looked very tired.
Speaking on ITV, Neville said: "For me last night the big problem was that James and Shaw didn’t deliver the creativity I thought they would and Foden and Sterling didn’t.
"They all looked physically exhausted, that was my biggest concern.
"I expected James and Shaw last night to be the creativity, especially with the acres of space in front of them because of the [Scotland] wing-backs."
Shaw was disappointed not to be involved in the opening game, when Kieran Trippier started at left-back, but struggled to make his mark meaning Ben Chilwell could come in against the Czech Republic.
The Manchester United full-back was asked about the misfiring Kane, but backed the England captain to bounce back.
"I have no concerns," said Shaw. "I personally think that he is the best striker in the world. He is a very important part of the team, in fact, the most important part of the team.
"Whether he is not at his best or not, he is a massive part of the team and a crucial player for us. His performances might not be as people expected but this can happen in tournament. He can score a goal in any moment and he is crucial on and off the pitch. He has our backing and he is the best in the world in his position. We have no worries at all."