Atletico took the round 16 tie into extra time before eventually winning the second-leg 2-3 - and the tie 4-2 on aggregate.
“What I have to say, and will be saying at the next UEFA coaches' meeting, is what I think is unfair," said Atletico boss Simeone.
“The rule favoured us today but it might go against us in the future. Liverpool had 30 minutes fewer to score an away goal. That's wrong."