Wade Elliott deservedly gave the visitors the lead before half-time, turning the ball in at the back post from Brendan Moloney's cross.
Sam Baldock added a second with his 24th league goal of the season before substitute Stephen Pearson scored with his first touch after 75 minutes.
Luke Freeman netted a free-kick for Stevenage late on to the annoyance of Cotterill.
"I'm not sure their goal was a free-kick to be honest," he said. "I'm not convinced of that, and we wanted the clean sheet which is a little bit disappointing.
"Going in 1-0 up at half-time was an absolute travesty really. I counted at least eight good chances.
"I thought that our concentration was going to be important going into the second half because we had so much of the ball.
"The danger is sometimes when it becomes like that, and you have so much of the ball, that you can lose concentration and get done with one ball.
"I said to Sam Baldock that I felt we needed a goal from him, not that he wouldn't want one himself, but I wasn't going to take him off until he did score.
"And there was a nice little moment for Stephen Pearson as well, he scored a great goal."