The Championship outfit crashed out of the cup, after losing 4-1 to Stoke City after extra-time in their third-round replay at the Britannia Stadium.
Zaha, who has been linked with a move to Arsenal and Manchester United, was booked for going down in the penalty area in the first half; a decision that angered his boss.
"There is only one thing that saddens me - that the referee dishes out a yellow card to my player who actually beats someone and got caught," said Holloway.
"We had to bring him off [at half time] because his ankle was hurt - did he make that up as well?
"I don't think so, but Wilfried Zaha has been labelled a cheat."
United boss Sir Alex Ferguson was scheduled to attend that match, but did not show up.