The Republic of Ireland midfielder was forced off at half-time after being injured by a Bradley Johnson tackle, for which the midfielder was booked, in the 2-1 defeat
McCarthy has impressed for the Latics this season and scored two goals in their previous match against QPR, which ended in a 2-2 draw.
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"It was an infuriating moment and something you don't want to see," Martinez told BBC Sport. "Clearly he was targeted. They got away with it. You don't want to see players injured in such a ruthless manner.
"James is an outstanding footballer and he's in a great run of form. He scored two goals in the last game [against QPR].
"It was clearly a cynical challenge without the ball to be played for. The referee saw it, showed a yellow card and I don't think he can do any more than that as a referee."
Martinez did admit frustrations with his own side's display as Wigan continue to seek their first win since their victory over Reading on November 24.
The Spanish coach was impressed with the way his team reacted to a poor first-half display, however, and was left to rue Wes Hoolahan's winning goal shortly after the hour mark.
"We never showed our true potential," Martinez conceded. "The start was sluggish and very pedestrian. We never got any rhythm going.
"I couldn't be prouder of our reaction in the second half. We controlled the game completely and I could see a real momentum building, but more soft defending cost us."