Adam Rooney had given Blues a first half lead from the penalty spot but Boro came out the stronger side in the second half scoring three times to inflict a second away defeat of the season for Hughton's side.
"Legs were tired in the second half, possibly because we had a difficult game on Thursday night in the Europa League," the Blues boss said after the game at The Riverside.
"But also we have lost three important players this week - Liam Ridgewell, Morgaro Gomis and Jordan Mutch.
"That left us with kids on the bench and unable to change it too much.
"In the first half we did well enough but in the second we tired, although we added to our own downfall by giving away a soft goal so early in the second half. There was no need to give away a free-kick there. That gave Boro the momentum.
"Was there a touch of offside about their second goal? Maybe, it was certainly very close. It was a fortuitous rebound for him.
"And we should have had a free-kick for a foul on David Murphy in the build up for the third but these things happen."