The Latics player, on his first Premier League start, caused outrage with a reckless knee-high challenge on substitute Massadio Haidara.
He escaped punishment but referee Mark Halsey sent off furious Newcastle assistant manager John Carver - who twice had to be restrained as he tried to confront McManaman at the end of the first half - and Wigan coach Graham Barrow in an unseemly fracas.
Newcastle have already had problems with their touchline behaviour this season after manager Alan Pardew was banned for two matches for pushing assistant referee Peter Kirkup and more Football Association action is almost certain to follow.
Martinez later insisted McManaman was not a malicious player despite his reckless challenge.
"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," the Spaniard said.
"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."
Martinez added: "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."
The incident adversely affected the game as from the moment Haidara was carried off on a stretcher the mood changed significantly.
Jean Beasejour's first-half goal had been cancelled by Davide Santon with 18 minutes to go only for Kone to snatch a vital close-range goal in a goalmouth scramble in which the ball appeared to come off team-mate Maynor Figueroa's hand.