Kerr, who recently returned from a long-term knee injury, was sent off for two yellow cards, the first for dissent and the second for his professional foul on Rashid Yussuff in the build-up to Wimbledon's first goal in their 4-3 extra-time win.
Kerr will miss Saturday's clash at Port Vale through suspension.
"It was a case of frustration with Scott," said Mills. "I haven't actually looked back at any incidents during the game, I've given myself a couple of days off with the players and come back in to prepare for Saturday.
"I wanted to get Monday completely out of my head. What's happened with Scott happened. It's one of the worst decisions I've seen from the referee. If he didn't give the corner, he should have given a penalty and he's not given either and given a goal-kick instead.
"So I understand Scott's frustration. I don't condone it, but I do believe him because he's an honest bloke and he said he just asked the referee why he had made that decision. That's as far as it's gone and that's as far as it's going to go."