Warnock was unhappy that referee Mark Clattenburg awarded a spot-kick against Tom Lees after his arm made contact with Sergio Aguero's face.
Aguero scored the penalty, and added another, as his goals plus strikes from Yaya Toure and Carlos Tevez sent Leeds out of the competition and sealed City's place in the quarter-finals.
Warnock admitted his team would have struggled to get a result at the Etihad Stadium but that the timing and nature of the second goal made life comfortable for the home side.
"It was such a soft penalty and I don't think the referee would have given a foul anywhere else on the pitch for that," he said.
"The second goal is always going to be crucial in any game and it was never a penalty in a million years but teams get them sometimes.
"They were still better than us but to get that second goal made it more comfortable for them and made it easier."
The defeat means Leeds' interest in this year's FA Cup comes to an end but Warnock urged his players to learn from their experience of playing at City and to be proud of a season of cup progress during which they eliminated three Premier League sides.
"It's a lesson for our young lads, the first 10 minutes of the game were very difficult," he said.
"But we've beaten some good sides in the cups this season, we've put out Southampton and Tottenham and we should be proud of what we've done in these competitions."
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