Latics forward McManaman, on his first Premier League start, caused outrage with a reckless knee-high challenge on Haidara, who was reported to be in too much pain to have the injury assessed after the game.
The Newcastle boss later revealed that referee Mark Halsey, who did not even book McManaman, had apologised at half-time for missing the challenge.
Pardew's annoyance was compounded in the final minute when Arouna Kone slotted in the winner after a goalmouth scramble, with the Newcastle players all appealing for handball on Maynor Figueroa.
"It is an awful challenge. The pictures speak for themselves," said Pardew. "I thought it was a bad challenge and I was 60 yards from the incident.
"The players knew because they were on top of it and there was a lot of bad feeling about that incident when it goes unpunished. He (Halsey) said 'If I've missed it I apologise' - that was at half-time.
"My job was to calm the players at half-time, not go looking for retribution, and try to win the second half - which to all intents and purposes we did.
"But again there's a decision at the end where we should have had a corner, it goes up the other end and there's a handball - that is tough to take."
When asked about the extent of Haidara's injury, Pardew added: "The doctor assessed him quickly before he was scuttled away to be assessed later.
"It looks like knee ligaments and bad bruising and that's the best we can hope for."
The Newcastle boss also has concerns over full-back Mathieu Debuchy who limped off with a hamstring injury and was replaced by Haidara.
"We will send him to France (for this week's international duty) for them to assess him but we think he will be on his way back," he said. "We don't think it is a particularly bad tear - a strain hopefully."
The incident resulted in Newcastle assistant John Carver and Wigan coach Graham Barrow being sent to the stands after a melee developed at the end of the first half.
"Remember it's Callum's full debut in the Premier League. I haven't seen the replay, I believe that he touches the ball and then it's a bad challenge, but it's nothing malicious, he's not that sort of boy," Martinez told Sky Sports.
"It's the normal enthusiasm that you get in your debut.
"I can't really comment too much because I haven't seen the action but I can guarantee that Callum McManaman is a young man full of talent and in his debut probably showed the enthusiasm that you expect, but he's not a malicious player."
Regarding an apology, Martinez said: "I think he wants to contact the player. I don't know if he's done it already but he will do that because when you get an injury in that manner you obviously don't want to leave any bad feelings.
"If Callum hasn't apologised yet then he definitely will do that because we're a football club where those values are very important."