McCarthy was on the sidelines for five weeks with a groin injury but played in Ireland's matches against Georgia and Moldova earlier this month.
Koeman acknowledged McCarthy was put in a difficult position when asked to determine his own fitness for the international fixtures and also urged Ireland manager Martin O'Neill to handle his players more sensibly.
"If you leave it up to the player to decide then he is in a difficult situation... You hope something like this would be solved by the understanding of the doctor of the Ireland team or the manager of the Ireland team," the Dutchman added.
"I like to have a lot of international players because it is a very good experience for every player. But sometimes, in several cases in fact, you like to have a little bit more understanding for a player... You are killing the player."
Fifth-placed Everton travel to Premier League leaders Manchester City on Saturday.
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by John O'Brien)
