Los Blancos had gone ahead when Vinicius Junior prodded home Federico Valverde’s cross in the 70th minute, but Girona found a way back when Marco Asensio was deemed to have handballed inside the box after VAR consultation.
Cristian Stuani stepped up to convert the spotkick, netting against Real for the third straight time, pinching a share of the points, with Toni Kroos sent off late for a second bookable offence.
Real were also denied a goal when Rodrygo poked home from close range, but the referee claimed goalkeeper Paulo Gazzaniga had the ball in his hand.
“I don’t like to talk about referees but I will today,” Ancelotti said. “The first situation is a clear one. It’s not a penalty because he doesn’t touch it with his hand.
“I asked Asensio and he said he never touched it with his hand, it came off his chest. The left hand was in an odd position.
“If he’d have touched it with his hand, there may have been doubts around it. He didn’t handle it, they’ve made it up.
“The second one is more open for debate. If the goalkeeper gets the ball in his hand, you can blow the whistle, or not. I won’t talk about that one.
“I’m most surprised by the penalty. It came at a crucial time because the game was all but wrapped up. We struggled to score goals, we didn’t play brilliant football and we found it tough to win the ball back.
“We had the chance to make it 2-0 through Asensio. This situation has cost us two points in the table.”
Real are back on top with 32 points, one ahead of second-placed Barcelona, who won 1-0 at Valencia.