Hughes watched the second half from the stands after complaining during half-time that his side should have had a free-kick in the build up to the crucial goal.
Coventry striker Cody McDonald shrugged off Peter Hartley to latch on to Carl Baker's through ball and strike the decisive blow in the 33rd minute.
Referee Fred Graham allowed the goal to stand but Hughes felt the he made the wrong call and stressed the wider importance of such decisions.
Hughes said: "It's pointless getting hung up on that because we still had 60 minutes to get back into the game and we couldn't get the ball over the line.
"You go back to that incident and you are saying to yourself that livelihoods are at stake and you are playing for your livelihood so you are just hoping the decisions are 100 per cent correct.
"I felt it was a free-kick. I felt the guy bumped him so to get beat on that is disappointing. I felt we were the better footballing side.
"The referees have got a hard job. I am not pointing the finger of blame at the referee.
"I spoke to him at half-time and he probably made his decision to send me to the stand on his emotions.
"Not once did I raise my voice, not once did I use foul and abusive language I just pointed out that livelihoods are at stake."