Muller said that things have been going so well for Bayern lately that such a defeat asks questions, but that in the long run losing might turn out to be positive.
"We're through, so the end result is a positive one, even if the result on the night wasn't exactly what we'd hoped for," UEFA.com quotes Muller as saying.
"To lose such an important game 2-0 at home throws up a lot of questions, especially in this fantasy world we've been living in for the past few months. In that respect, maybe it's not such a bad thing because it will prompt us to think more about ourselves as a team.
"We had a few good spells tonight and really should have scored. In fact, we didn't play that badly at all, but the fact that we conceded a second goal towards the end and had to endure a nervous last five minutes or so shows that something obviously went wrong."
Muller has scored 16 goals in 30 appearances for Bayern this season.