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The Dutchman left Rashford on the bench for the trip to Molineux, despite the 25-year-old scoring two goals in two games after returning from the World Cup.
He was introduced as a half-time substitute, however, and went on to score the winning goal, before having a second ruled out for handball after a VAR review.
Speaking to BT Sport after full-time, he said: "I was a little bit late for a meeting - I overslept.
"It's the team rules and it's a mistake that can happen, but I'm disappointed not to play, but I understand the decision and I'm happy that we managed to win the game anyway.
"I think we can draw a line under it and move on.
"I'm in a good place and I'm just pleased with the way that we're progressing. In the past, we could easily have lost that game or drawn it."
Ten Hag was also questioned on the decision to leave Rashford out.
In his post-match interview, he said: "After the decision, he came in, he was bright, he was lively, he scored a goal - that is the right reaction.
"Of course [that is the end of the matter], but everyone has to match rules and values and, if you react like this, this is the right answer."
The United boss was questioned further in his press conference on whether it sent a reminder to the squad to keep their standards high.
"That is how it has to be," Ten Hag added. "We are a team that is hard to beat but that is because we are attacking with 11 and defending with 11.
"That is because everyone is following the rules. If you don't do that anymore, if you don't follow the rules, it flows onto the pitch.
"I was not satisfied with the performance [before Rashford was introduced]. I think we had chances. We created them but we didn't [take them].
"I think we have to be more clinical in front of goal. We know Rashy can score the goals and he did.
"It is a responsibility for individual players, some were not ready. If not front foot and focused you have problems."
Cristiano Ronaldo was also subject to disciplinary action in his final few months at Old Trafford and, following the Portuguese's move to Al Nassr in Saudi Arabia, Ten Hag said success demands effort across the board.
"I don't talk about the past. Let's talk about the future," he said.
"We have taken a good step - the first time in the top four. But there is a long way to go. We have to win every game to get into a position where you can win something.
"That is what we are aiming for. It demands hard work from everyone."