A penalty from Ben Watson, controversially given after a Matt Mills handball, and Nick Powell's brilliantly executed overhead kick gave the hosts a 2-0 lead inside 24 minutes.
However, Wanderers clawed themselves back into the game and after Neil Danns and Andre Moritz, from the penalty spot, had brought Freedman's side level, Callum McManaman's strike was required to give Uwe Rosler the perfect DW Stadium start.
"As soon as the second goal went in we showed too much emotion and that hurt us," said Freedman.
"That's the most disappointing thing. Apart from that the lads have got to take huge credit for the spirit they showed. The result wasn't to be with us today but the performance certainly was. If you've got a team playing like that the results will pick up."
As is usually the case in a typically feisty derby affair, the contest did not pass without incident.
Freedman was perplexed by referee Kevin Friend and his assistant for their collective U-turn in awarding Latics a first-half penalty when a cross struck Mills' arm, a decision he felt was influenced by a host of blue and white shirts surrounding the official.
Freedman added: "It's very, very hard to take when the referee has gave a corner, the linesman's given a corner.
"Five or six Wigan players have surrounded the referee which is not in the rules, not one of them has been booked, then he's changed his mind 30 seconds later.
"The linesman has changed his mind from 45 metres away to now gave a penalty. Is he hearing through the microphone? I don't know, he's surrounded by players. The perception is he's let me down."