The Spaniard was called for a violation of the 20-second rule at deuce while the match against Kei Nishikori sat at 4-4 in the third set.
"I don't want to change the rule," BBC Sport quotes Nadal as saying. "I accept that sometimes I was slow. I respect that. The negative thing in my opinion is not the warning, but the timing of it.
"You can choose another moment to do it, not that one. She didn't advise me before the second warning that I was still going slow. It's a normal thing, for the referee to help the player a little bit, and say, 'Rafa, you are going too slow'."
Nadal will take on Grigor Dimitrov in the quarter-finals.