The referee initally gave a corner kick following Matt Mills handball early in the first half. However the howls from the crowd and the reaction of the Wigan players suggested otherwise and he was swift to change his mind under influence from the assistant referee.
Despite this, Freedman was critical of the Wigan players who crowded round the referee as he was making his decision.
The Bolton boss said: "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."
Freedman was also pleased with his team's response as they fought back from two goals down to level the scores before eventually going down 3-2.
"As soon as the second goal went in we showed too much emotion and that hurt us," added 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."
The result leaves Bolton in sixteenth place in the table, three points behind the Latics who lie in fourteenth place.