"At the moment I cannot defend myself because we are out of the Champions League," Van Gaal told a post-match news conference.
"Every word I say is wrong. But when you see the facts, we were further in the (League) Cup (than last season), qualified for the Champions League group, we have played all these matches and are still in a very good position in the league.
"We are better than last year. That's my answer because I can only give facts. I'm also disappointed that we are out of the Champions League."
Anthony Martial put United in front in Germany but centre back Naldo equalised and Wolfsburg took the lead before halftime through midfielder Vieirinha, who finished off a slick passing move with a tap in.
United clawed their way back thanks to Josuha Guilavogui's late own goal but Naldo struck again to seal the win, while Dutch champions PSV Eindhoven beat CSKA Moscow 2-1 in the other group fixture to advance at the Premier League side's expense.
"It was a crazy match," Van Gaal said.
The manager's woe was compounded by injuries to defenders Matteo Darmian (hamstring) and Chris Smalling (groin), which he said would likely rule them out of Saturday's Premier League game against Bournemouth.
Van Gaal was especially unhappy with midfielder Bastian Schweinsteiger, who he was banking on before the game to guide United through to the knockout stages.
"I cannot say that he was the Schweinsteiger from my period in (Bayern) Munich in this game," Van Gaal said. "I have changed (substituted) him and I don't change players for nothing."
Van Gaal himself was heavily criticised, with Rio Ferdinand adamant that United did not deserve to qualify.
"When you think of the money they have spent you can understand the fans' frustrations. The pressure is growing on Louis van Gaal now," the former United defender said on BT Sport.
Paul Scholes echoed Ferdinand's sentiment.
"United are just an average team and with an average team you get average performances. You have to say they have not bought as well as they could have done," the former United midfielder said.
(Reporting by Simon Jennings in Bengaluru; Editing by John O'Brien)
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