The former Premier League champions go into the final game of the Championship season in the final relegation place, tied with Nottingham Forest ahead of their clash at Brentford on Sunday.
Nonetheless, their chances of survival were not helped by Birmingham's 2-0 win over Huddersfield on Saturday when Wagner, with one eye on the playoffs, made 10 changes for the game.
Mowbray told Sky Sports News: "I fully understand the decision, to be honest. I've been a manager a long time now, and particularly in cup competitions you make eight, nine, 10 changes to give your squad a game.
"I think the manager at Huddersfield has seen it as job done, we've made the playoffs, and he's been able to pick a team for a game which doesn't really matter. What matters is trying to win the playoffs. I understand his reasoning but the bigger picture is the integrity of the league.
"I could sit here and say 'Oh I was really good friends with [Brentford boss] Dean Smith and I've had a chat with him, he's going to put his kids out on Saturday' but how would that appear to Nottingham Forest or Birmingham City?"
"It doesn't happen. We've all got a right to go and try to win every game. David Wagner probably thought he could go to Birmingham with the team he put out and win... it doesn't matter, I feel as if I can sit here bleating about it but we have to look after ourselves."
Birmingham sit 20th in the table on 50 points, while Forest and Blackburn are in 21st and 22nd respectively on 48 points, with the Reds' goal difference better by just one.