Hughes was sacked on Friday, and new boss Harry Redknapp watched the Old Trafford defeat from the stands, leaving Bowen to run the show for one match.
"People ask me what went wrong but when this club stayed up on the last day of last season, clubs like Southampton and Reading had a better squad than us," said Bowen.
"They had players who had been together and had success together. At times we have been criticised for the number of players who have left.
"Not one player we have let go is anywhere near the Premier League now. We have brought good players into the club. I have seen it every day in training. Maybe at times a few of the lads have been found wanting."
He added: "I have not spoken to Harry and he has not spoken to the players. It has been difficult.
"Football is an emotive game and Friday was a desperate day. Mark is my friend. I just said I would prepare the team to give everything it has got."
Bowen denied reports Hughes had walked off the training ground on Friday, having been informed by chief executive Philip Beard he was going to be sacked no matter what the outcome of Saturday's game.
"We were preparing for training and putting our ideas together about what we were going to do when Philip knocked on the door," he said.
"No-one was called over. It was all handled with dignity."