Trotters substitute David Ngog scored a second-half brace to push the Addicks back into the bottom half and below their opponents into 14th.
He said: "We were disappointed because we grew into the game and created the better chances.
"Bolton have obviously come down from the Premier League and that always makes it a difficult game.
"We are good away from home and we got the right balance between attack and defence throughout the game.
"In the end, though, we were beaten by a substitute who has a huge pedigree in the game and he has made a huge difference.
"I'm sitting here thinking that we should have won that game but we'll be looking to go into the Christmas period trying to bounce back from a defeat which shouldn't have happened."