A 43rd-minute header by James Husband gave Rovers a point after skipper Josh Simpson fired the hosts ahead at the Broadfield Stadium.
Rovers 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."
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.
"We've 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."
Like Rovers, Crawley have now also gone four matches without a victory, but boss Richie Barker felt his men were unfortunate not to have taken maximum points.
He said: "We deserved to win the game to be honest. The players were absolutely fantastic and their energy levels were excellent. We felt we could move the ball quicker, with more pace, and that proved right."
Barker admitted his only disappointment was the manner of conceding the goal and losing goalscorer Simpson with an ankle injury.
He added: "I'm delighted with the way the players put their bodies on the line. But we defended far too deep when Doncaster got their goal. But they got a little bit frustrated at the way we moved the ball around."
- Sports & Recreation