A 43rd-minute header by James Husband gave Rovers a point after skipper Josh Simpson had fired the hosts ahead at the Broadfield Stadium on Monday night.
Doncaster have failed to win in four games and Flynn responded to his side's display by locking them in the dressing room for 50 minutes.
The Welshman emerged to admit: "I'm very disappointed with the performance and to be brutally honest we are lucky to come away with a point.
"In terms of chances created, it's been a problem in our last two games and we need to improve against Yeovil on Saturday.
"We're still second but we've missed the chance to go top. It's important that the players have had a chance to air their views and we must do better."
Flynn is hoping to make three additions to his squad this week and added: "I've lined three up and they've agreed in principle. I'm looking at all areas."