Germany led 2-0 after a 52nd minute penalty from Ilkay Gundogan and a goal from Kai Havertz in the 67th, but that advantage was wiped out in just over 15 minutes.
Luke Shaw struck in the 72nd, Mason Mount equalised three minutes later, and a penalty to Harry Kane put the English up 3-2 in the 83rd.
Ultimately, an 87th-minute leveller from Havertz saw the two sides share the points, and it gave Flick some mixed emotions.
"The first half was balanced, in the second we deservedly led 2-0 – then we made individual mistakes," he said. "It must not happen that we give up a lead like that.
"But we came back, that's the positive. It was a good test, we take a lot of positive things with us, but also negative things. There's some work for us to do, but we're optimistic, otherwise we could stay at home."
Midfielder Joshua Kimmich provided a little more insight into exactly what went wrong to allow such a rapid collapse.
"We had everything under control and deservedly led 2-0 – then we became far too passive," he said. "No longer pushing through consistently, defending far too deep, no longer having the courage to play against the ball… but in terms of body language and engagement, it was an improvement.
"Everyone now has six weeks to get a good feeling and then we will attack."
After scoring two goals, Havertz said to only get a draw from a match like that "must of course worry you" but suggested that it "was another good game to learn from".
Meanwhile, Gundogan was not afraid to talk about Germany's lofty goals, saying they are heading to Qatar with the plan of making the final.
"It's not unrealistic," he said. "Of course, a lot has to come together. I don't see a team that is miles ahead.
"We have shown over long periods that we can do it at the highest level. We have to try to do that for 90 minutes. At a World Cup you have much less leeway to make mistakes than today."