The incident led to angry scenes at The Den as both players and manager surrounded the ref at the final whistle, amid cries of "Cheat" from the crowd.
Speaking to the club's official website, manager Dennis Wise revealed that Penton accepted that on this occasion, he got it wrong.
"I've actually seen the video and had a look at it," said Wise. "On the video it clearly shows that the referee blew up before the ball went in the net.
"I've gone in to see him after the game and asked him to tell me why? Basically, he held his hands up and said 'I've made a mistake, I should have given a penalty. I blew up before the ball even went in the net and had made the decision and then gave the goal.'
"I know that Andy Marshall stopped for a split-second and it was a bizarre incident. In one way you have to give him some credit for admitting his mistake to us because a lot of referees and linesman don't admit to their wrong-doing. He's made a mistake, he's wrong and he has apologised to us, but obviously that doesn't get us three points.
"Hopefully this doesn't cost us in the long run, but we will have to wait and see."