England midfielder Mount, who managed just five top-flight starts in his first season at Old Trafford, was withdrawn at half-time at the Amex Stadium due to a fitness issue.
United looked set to come from behind to win on the south coast after Amad Diallo cancelled out the 100th career goal of former United forward Danny Welbeck.
But, following a bizarre disallowed goal involving substitutes Joshua Zirkzee and Alejandro Garnacho, Seagulls striker Joao Pedro compounded the visitors’ misery by heading home in the fifth minute of added time.
Asked about Mount’s withdrawal, Ten Hag: “It was forced. He mentioned an issue and I didn’t want to take the risk with him.
“I don’t how much of worry it is, I can’t say at this moment. Maybe it’s nothing but when we have a good bench then don’t hesitate, bring him off.”
Following Diallo’s leveller, Zirkzee went from hero to zero by preventing Garnacho from turning the game around in the 70th minute.
The summer signing from Bologna, who came on for Mount after last weekend scored on debut to earn a 1-0 success against Fulham, touched home his team-mate’s goal-bound finish on the line while in an offside position.
VAR duly intervened and Pedro was then left unmarked in United’s penalty area to nod in Simon Adingra’s cross and give Brighton boss Fabian Hurzeler victory in his maiden home game in English football.
“Of course we can bring this goal back and explain it in detail what has happened,” Ten Hag said of the disallowed goal .
“The most important is we have an overload and then it’s about doing the final pass, players in the right positions, get the right finish. I think everything we did well there. It’s misfortune.”
Speaking about the defending of Pedro’s winner, Ten Hag said: “We have to talk about this, how we act in that situation as a team.
“There was more than one mistake in that occasion and it has a big impact on the score.
“If you can’t win – and I think we were close to winning this game – then definitely don’t lose the game.
“Both goals are very soft goals we conceded and, as a team, we should have done better.”
German Hurzeler described the disallowed goal as a wake-up call as he savoured a landmark win on the back of a 3-0 victory at Everton.
“After we conceded the goal, we lost the control of the game,” said the 31-year-old.
“The game was too open and that’s one of the biggest strengths from United. It was lucky we didn’t concede the second goal after the VAR decision.
“It was a wake-up moment for us and then we started to control the game again and how we played the last 10, 15 minutes was amazing.
“I’m very happy the players had the attitude of never giving up and always believing in their own strengths and in each other. I could feel it on the sideline.
“My team deserved to win. These moments make memories and we have to enjoy it.”