After waving away initial penalty appeals, referee David Coote was sent to the pitchside monitor by the Video Assistant Referee to review Matthijs de Ligt’s challenge on Danny Ings.
After a lengthy stoppage, Coote pointed to the spot and ignored protests from United’s players over a handball by Ings before Jarrod Bowen converted the penalty in the second minute of injury time.
“Before the season there was the instruction about VAR only interfering in clear and obvious mistakes,” Ten Hag told BBC’s Match of the Day.
“That is definitely not a clear and obvious mistake from the on-field referee.”
United dominated possession and had the better chances in the first-half, with Alejandro Garnacho striking the crossbar and Diogo Dalot missing an open goal.
“We have to look in the mirror, we don’t score in a good game from our side. Create loads of chances and concede none, but when you lose in this way it’s a bad feeling,” Ten Hag added.
“Unfair and unjust the way we conceded the penalty.”
The Dutchman said he had spoken to the officials after the game at London stadium
I spoke with them. But the decision is made. There’s no way back and that’s football,” he said.
“That’s a third time I have felt injustice in the season and it has a big impact on our team and on our scores and where we are in the table. It’s not right.”
The result moves West Ham up to 13th in the Premier League, one place above Manchester United who have won just three of their opening nine games.
Asked about the penalty decision, West Ham boss Julen Lopetegui said: “I didn’t see it. The players say it’s a penalty and the referee says it is a penalty, so I am sure they are right.