Ronald Araujo saw red as Chelsea won 3-0 on Tuesday night.
Afterwards, Flick said: "We started really well and had a big chance to score the first goal (when Ferran Torres shot wide). We know that Chelsea are a really good team and with one player less, it's not easy to win here.
"We tried everything. The way we defended as a unit was OK, but in the end we made too many mistakes. This is what I can say now, but we have to analyse everything. We have to make things better, while under pressure."
On the danger of missing the knockout phase, Flick insisted: "It's just now about getting into the next round. This is our goal. If we can win nine points, everything is possible.
"We will see, but we're looking match by match and next is Frankfurt. I'm really positive because we've got players coming back now and there are three games to play and nine points to win."