Izale McLeod's first goal since rejoining the Dons and superb half-volleys from Daniel Powell and substitute Stephen Gleeson sealed a first win in nine games for Karl Robinson's men.
And Flynn was grateful his overnight leaders escaped with only a three-goal defeat at stadium:mk after a dismal display.
He said: "We lost to the better team. On the night they were better than us, the way they controlled the ball, their movement was always a problem for us and we just didn't deal with it all night.
"It was a really harsh lesson for us. We should have retained possession better, that's for certain - we didn't do that from the first minute to the last so that was a dangerous sign coming through.
"When you have so many players having an off-day it's not going to work for you, that's for certain. We struggled defensively - they've hit the post twice and they've had other chances. It could have been a heavier defeat.
"I think it was an all-round particularly bad night for us. There were no harsh words in the dressing room, just honest words - that's the key to it.
"If there's a small crumb of comfort it's that we're still top of the league and if you look at the recent month we've been five games undefeated."