And he said several of his players were off form which Walsall couldn't afford against a good Stockport outfit.
He said: "Sometimes you have to hold your hands up and admit you were well beaten.
"It wasn't a terrible performance by us but wew didn't do enough to win and now it will be all about how we deal with losing the game at home when we have another one coming up against Mansfield.
"I may have to look at changes, some of them might be enforced but I will be expecting a response from the players."
Danny Johnson won't be playing against Mansfield on Sunday but it remains to be seen whether Liam Bennett will be in the squad.
Reports from Cambridge indicate he may be recalled by his parent club but Flynn said the situation is uncertain.
He said: "I haven't heard anything though I am expecting to tomorrow - it will be a sham if we lose him he has been great for us, a model professional and has performed well but we will have to see."