Despite getting the three points, Van Gaal was not happy with the performance, especially the way his team surrendered control after going ahead.
"In the first half we played very well but we didn't finish our chances, and that was our problem," he said.
"It was 1-1 at halftime but we created chances to be 3-1 ahead. Then you have to continue and we did, but only for the first 15 minutes, I think.
"After the goal it was transforming our team, because we didn't keep the ball anymore and I didn't see Wolfsburg pressing so much, so we gave the ball away," he added.
The Dutchman bemoaned United's lack of killer instinct and said teams do not win the Champions League without it.
"You shall win the Champions League when you are clinical and when you can finish the game much earlier," he added.
"We had the chances to do that in the first half, or to keep the ball in the second half. We didn't do that and I was suffering on the bench, but the fans were also suffering and I have to admit the players were also suffering.
"But they continued with the team spirit."
With CSKA Moscow's 3-2 win over PSV in Russia, all four teams in the group are level on three points after two matches.
United, top of England's Premier League, have now won four games in a row in all competitions, scoring 11 goals and conceding three.
Van Gaal's thoughts have already turned to their league clash with Arsenal on Sunday.
"We have to recover, recover and recover because Sunday is Arsenal and they played yesterday, so they have one more day of recovery."
(Reporting by Simon Jennings in Bengaluru; Editing by Peter Rutherford)
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