The Italian boss was unhappy after the full-time whistle at Mestalla, despite watching his side emerge with a vital victory
Goals from Ezequiel Lavezzi and Javier Pastore had put the visitors in a commanding lead, but a stoppage-time strike from Adil Rami and the dismissal of the Sweden striker gives the home side hope ahead of the second leg.
"Our third goal should've have stood," Ancelotti told Canal+.
"Ibrahimovic's red card was not deserved. I don't understand it. It's not fair.
"We conceded a goal and Ibrahimovic got a red card and I don't think that he deserved it because it was a normal tackle. And so, because of this, we are really disappointed because the play was really good, we played really well, focused on the game, and for this we have to be happy but the end of the game was not good for us.
"I think it was a normal tackle, nothing special, I was surprised to see a red card."
The Italian boss also admitted that his side could not afford to fall victim to complacency when Valencia visit Parc des Princes in the second leg of their last 16 tie.
"Valencia are a good team and we have to know that we have played just the first half of this game, and we have to play the second half at home," he added.
"It will be better for us, but we have to pay attention."