McCarthy will be out for up to 10 weeks with an ankle injury after a challenge by Muamba in the 1-1 draw on Saturday.
Wigan boss Roberto Martinez has claimed the tackle, while not malicious, was "unnecessary" and "reckless".
But Coyle told Radio 5 live: "Fabrice is a very talented player - he went to try and win the ball, that's all."
In stating that he would never condone bad tackles, Coyle added: "The last thing we want is players getting injured.
"Fabrice felt he had an opportunity to win the ball.
"We have to eradicate bad tackles, but I think it was a young boy who went to win the ball and he never had any intent to try to hurt James McCarthy."
Martinez later, said: "One of the most creative young players in the league is going to be out for up to 10 weeks. That is a football crime."
Coyle, though, said he was surprised by his counterpart's comments.
"Maybe with hindsight he's come out and he's protecting his club," Coyle said.
"[But that's] the reason we love football, we love opinions and Roberto has got his and I certainly have mine."