Clint Hill thought he had given the visitors the lead in the 19th minute when his header from Joey Barton's corner clearly crossed the line before it was clawed out by Adam Bogdan, but neither referee Martin Atkinson nor his assistant gave it.
The FA released a statement during the match reiterating their "strong desire to see goal-line technology introduced as soon as possible", but Hughes was not impressed by the timing, and he said: "I think that's absolutely ludicrous that they come out and try to protect the poor performances of the officials they supply us. It's a joke."
Darren Pratley opened the scoring for Bolton in the 37th minute and, although Djibril Cisse equalised just after half-time with a goal that was shown to be offside, Ivan Klasnic netted the winner four minutes from time to lift Bolton above their opponents and out of the relegation zone.
Regarding the display of Atkinson and his assistants, Hughes said: "All you ask for is the key decisions in games to be judged correctly and I felt that wasn't the case all day.
"Martin Atkinson's acknowledged as one of the better referees and his performance was okay but I thought he was let down by his assistants.
"Obviously from our point of view to have that clear goal chalked off was a significant moment. Don't underestimate the significance of scoring first. We're the away side, we're at the wrong end of the table and to score first is crucial for us.
"If we scored then I think we would have taken the game away from Bolton because they would have had to come out and try to get back into the game. Not getting a decision of that magnitude correct impacts on what we feel we can get out of the game.
"In fairness they even got our goal wrong because that was slightly offside so they haven't covered themselves in glory.
"They missed a penalty, they missed a handball in the area. In the end I think the guy on my side completely lost his nerve to make any decisions."
Source: PA
Source: PA