Wanderers remain searching for their first home victory and slipped back down to 21st in the Sky Bet Championship table - just two places above their winless opponents.
But Freedman was content with his team's display and insisted it is just a matter of time before the Trotters triumph at the Reebok Stadium.
"We started very well and we were playing some fantastic stuff and Jermaine scored a beautiful goal, but once again at home there was a huge piece of misfortune for us with the own goal," he said.
"I thought that we coped very well at the back and probably won the battle in the air at the end against a very good Sheffield Wednesday front four.
"We are playing very well at the minute and we showed great courage to get in their and try and force a winner and we had four or five really good chances to do that in the end."
Wednesday manager Dave Jones was angry with the officials after Jermaine Johnson's headed goal was disallowed and Jose Semedo was sent off.
On the red card, Freedman added: "As soon as anybody leaves the ground then you run the risk of being sent off.
"I've seen the video and he's jumped off the floor and committed a dangerous tackle on Jay Spearing.
"For the goal the guy's a yard offside and the assistant referee's done very well to spot it, to be fair."
- Sports & Recreation
- Jermaine Beckford
- Alex Baptiste