Having fallen behind to a Juan Mata strike, Swansea boss Garry Monk brought Ki Sung-yueng on for Wayne Routledge, changing the shape of his team in a bid to find an equaliser.
Two goals in the space of five minutes followed, from Andre Ayew and Bafetimbi Gomis respectively, as Swansea recorded a third-consecutive 2-1 win against the Old Trafford club.
“After 1-0 they changed the shape and then we could not cope with that, so that’s not good,” Van Gaal told Sky Sports. “For five minutes we lost our dominant role and that was a pity because I think we controlled the game.
“When you don’t know it [the formation] then you have to be compact.
“You saw Swansea in the last 20-25 minutes, they were compact and it’s always difficult to beat a compact team.
“We could have scored much more goals, so I don’t think that’s the problem. When you create chances that’s the biggest issue, and you also need a little bit of luck.”
Asked for his view on Swansea’s goals, Van Gaal added: “When the opponent scores a goal you can always find errors but I have to analyse that with my players.”
Meanwhile, Van Gaal has said he takes on board advice from Manchester United captain Wayne Rooney, hailing the Englishman’s brutal honesty.
“He is the most social guy and also very responsible,” Van Gaal said.
“I think he trusts me, so that is very important and I trust him, so when he comes to me and has remarks I always pay attention to them.
“He also has the confidence to say things that are not always normal for players to say, so that is also good for the atmosphere in the dressing room.
“He fulfils my expectations unbelievably well. I am very happy and proud of him. As a player, he is the example for everybody because his mentality is from a very high level.”
Van Gaal said being labelled ignorant of other people’s views surprised him.
“I am amazed you say I am single-minded,” he said.
“I have a philosophy. You have to come with good arguments to change my philosophy but when you have a better argument than me I change.
“I am an open guy. I speak about everything, but also with all my other players.”
Rooney scored his first goals of the season with a hat-trick at Club Brugge, ensuring United’s progression to the UEFA Champions League group stages – but a Premier League goal remains elusive three games in.