Newcastle manager Alan Pardew was unhappy with referee Mark Halsey's performance after the official missed Callum McManaman's "awful'' challenge and compounded his error by failing to spot a handball for Wigan's winner.
McManaman clattered knee-high into Massadio Haidara, who was subsequently carried off on a stretcher with suspected ligament damage, but the youngster escaped punishment in the first half of the Latics' vital 2-1 win.
The 20-year-old's challenge provoked anger from the Newcastle bench at half-time with assistant manager John Carver being sent to the stands - along with Wigan coach Graham Barrow - after twice trying to confront McManaman in an ugly melee.
To add insult to considerable injury, Arouna Kone's 90th-minute winner - after Davide Santon had cancelled out Jean Beausejour's first-half opener for the hosts - appeared to come off Maynor Figueroa's hand in the build-up.
"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. If it goes unpunished it doubles the impact on the mentality of the players and the team and it did have an impact on us, you can't get away from that.
"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.
"The linesman is looking right at it, the referee is there and all our players reacted and in that split second we didn't clear the ball - that's what happens when you miss a decision as big as that.''
Haidara was transported back to Newcastle while the second half was under way in order to be examined as soon as possible.
"The doctor assessed him quickly before he was scuttled away to be assessed later,'' added the Newcastle manager. "It looks like knee ligaments and bad bruising and that's the best we can hope for.''
As for the incident which saw Carver and Barrow sent to the stands, Pardew added: "I have no idea. I heard a kerfuffle outside, that's all I know.''
The Newcastle boss also has a worry over full-back Mathieu Debuchy who came off with a hamstring injury.
"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.''
Wigan manager Roberto Martinez defended McManaman and his team and does not think the striker will be retrospectively punished.
"Remember Callum McManaman was making his full debut in the Premier League and, as a young man, you know you are going to give your life for everything,'' said the Latics boss. "I haven't seen it but I believe he gets the ball and then it's a bad challenge.
"No-one wants to see that but I guarantee that is just a striker trying to win the ball over-enthusiastically because he is making his (full league) debut. What you need to look at in those incidents is if there is intention, a nastiness about the tackle. We are not a nasty team.
"He has not a nasty bone and is not bad-intentioned. The referee was in a perfect position, he is looking at the incident, where the ball is and where the ball is hitting. When you get the ball and then there is a follow-up it is very difficult for a panel to punish that.''
Martinez was critical of the half-time melee which saw Carver try to confront McManaman, something which continued in the tunnel and resulted in Barrow also being sent off.
"I have not seen it but it is something which should never happen,'' he added. "It is not for anyone to take justice into their own hands.''
The controversy overshadowed what was a vital win for Wigan - their first at home since late November.
"It was a day that we knew we needed to start showing a different type of character at home,'' Martinez added. "Our home form hasn't been good enough in terms the points we have collected not because of the quality of our play.
"We had to show an incredible character to get the winner and probably we got a little bit of luck, which is probably what we deserved because over the course of the season we've not been a lucky side.
"The reverse fixture at St James' Park we had a couple of really difficult decisions (Figueroa was controversially sent off) to take so it was really pleasing to get three points so late in the game.''