Wanderers were leading 2-1 when Kettle sent off Sam Ricketts for a second bookable offence. He then dismissed Craig Davies in injury time after he picked up two quick yellow cards.
“The sendings off were difficult to take because I don’t think Ricketts’ first caution was one,” Freedman said.
“The referee is only part-time and it’s difficult for him to keep the intensity.
“But we put the referee in a position where he had to make the decisions. We had a good start and played well, we should have been more up, Charlton came at us well. The crowd got behind them.
“I can only control what I can control and pick a team for Huddersfield on Monday. I’m confident – we’ve not lost ground.
“I strongly believe if we can win a couple of games and put pressure on other teams, we can get back. This showed it’s possible we can be in the play-offs.”
Goals from Johnnie Jackson, Dorian Dervite and Yann Kermorgant were enough for Charlton after Bolton had led 2-0 through Marvin Sordell and Medo Kamara.
Morecambe have no fresh injury concerns ahead of Tuesday's Sky Bet League Two home clash with Colchester.