Keane suggested Everton may be placing pressure on Coleman and McCarthy in order to prevent them playing for their country.
Neither featured in last month's fixtures with Gibraltar and Germany, but both played in Everton's subsequent 3-0 Premier League win over Aston Villa after that international break.
Midfielder McCarthy also sat out last Friday's 1-0 loss to Scotland with a hamstring complaint - a defeat that leaves Ireland fourth in Group D.
And, while claiming he had not read Keane's comments, O'Neill gave his own stance on the issue.
"I haven't picked up on Roy's comments," he said. "I don't follow him around. I haven't had the chance to read what he has said.
"From my own perspective, regardless of what Roy has said, I think the situation was this: way back the two lads were not fit for the games against Gibraltar and Germany [in October], and obviously played for Everton a couple of days later. That is understandable.
"I had spoken to Seamus and Seamus just wasn't right. I didn't speak to James at the time, but there was a thought that he might have played against Manchester United then, but didn't do so.
"I hadn't really a problem with that at all, it was just that this particular time, James does have a muscle injury. He came here, he was wanting to try it and really wanted to give it a go.
"We always thought that time would be against us and I think he will be perfectly all right to play at the weekend for his club, and really there isn't much more I can say about it."
Everton chairman Bill Kenwright had earlier told Sky Sports News: "I'm a big fan of Roy Keane's, but he does say some stupid things.
"That is just totally totally unfair. We absolutely love our players going on international duty and we never ever get in the way of them and Roberto Martinez will be as shocked as everyone at Everton."
Ireland face United States in a friendly on Tuesday.
