A brace from Ipswich loanee Kevin Lisbie sealed the Us victory at the Weston Homes Community Stadium to extend Colchester's unbeaten run under Aidy Boothroyd to nine matches.
Lisbie struck home his second goal from the penalty spot, after Josh Payne had been tripped by Hughes in the area.
Hutchings said: "I don't think that the decision was disputable but it was a poor decision in that the ball was going away and that was what cost us the game. You can't give away chances like that and it was an easy chance for them to take the lead again."
He added: "In the first half we got some great balls into the box but didn't get on the end of them. I thought that we were the better side in the first half and passed it better than they did.
"We had a few chances and I thought that they scored against the run of play. But I was delighted with the reaction that we got because we went straight back out there and equalised."