The Whites, backed by over 4,500 travelling supporters at the DW Stadium, came back from two down at half time after a penalty from Ben Watson and a Nick Powell overhead kick set Wigan on their way, despite controversy surrounding both goals.
A spirited second half performance led to Bolton drawing back through Neil Danns and Andre Moritz, but the Latics had the final say with a cruel blow 22 minutes from time as Callum McManaman’s deflected effort confirmed the win.
“I'm disappointed, we lost a game today that we shouldn’t have lost,” Freedman said. “I am disappointed with the perception of the first Wigan goal.
“I am not criticising the referee’s decision because it is such a hard job to do, but when he gives a corner and five or six Wigan players surround him, it changes the perception of the incident.
“We also feel the second goal is offside. We found ourselves two goals down and our spirit and positive play got us back into the game.
“In the second half we kept on going and we got level. The disappointing thing for me was for five or ten minutes after our equaliser we lost our shape.
“In the games we have lost recently there has been one goal in it and it is very narrow margins. It is my job to get the team organised.
“We pressed the ball right today and we created opportunities. We had enough chances to win the game in my eyes but we didn’t take them.
“Our rotation in midfield today was fantastic, which allowed Andre Moritz to get on the ball. Neil Danns also had a big game in the second half with his deep runs.
“At the end of the day we lost, there are no excuses and in all honesty I wish we had a game tomorrow.
“We have to start taking more of our opportunities but we are playing the game in the right spirit.”