The 20-year-old was at his flying best at Turf Moor but failed to break the Clarets' resilient defence, who got their rewards when Junior Stanislas fired in his first goal since September with 10 minutes remaining.
Zaha has been attracting attention with his displays this season and Holloway, whose side remain in the play-off places, claims he does not know if he will stay at Selhurst Park beyond this month.
"We will wait to see what Wilfried, if he ever does, actually goes for and we can talk about that if and when it happens," said Holloway.
"Wilfried beats people and gets brought down and that is very frustrating for him but he has to learn to deal with it.
"You are asking a young referee to make some decisions and I think he got some of those wrong.
"I am pretty upset with the referee, who, as the away manager, didn't do me any favours whatsoever.
"I thought we were fantastic in the second half. The goal came against the run of play but how we haven't got at least a point I don't know.
"I think there was a spell in the first half where our positioning wasn't good enough, but that got better and we looked bright.
"We pinned them back into their half but unfortunately I thought their defence played very well."
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- Junior Stanislas