The Spanish champions went down 2-0 to Jurgen Klopp's men after first half goals from Diogo Jota and Sadio Mane.
Atletico Madrid's task became even harder after Liverpool established their two-goal lead when Felipe was sent off nine minutes before half time.
The Rojiblancos also had Antoine Griezmann dismissed in the reverse fixture when Liverpool won 3-2 at the Wanda Metropolitano.
Atletico Madrid have now fallen into the Europa League zone and must get favourable results in their final two games against FC Porto and AC Milan to have any chance of reaching the last 16.
Simeone was not impressed with the way referee Danny Makkelie sent off Felipe, with Luis Suarez also having an effort ruled out by VAR in the second period.
"It is difficult for us to form an opinion. Firstly, because we didn't see the actions very well", Simeone told reporters after the game.
"The one from Griezmann [in the last game] was very quick. Of course, you could see later on TV as you probably have seen Jota's one tonight [Wednesday], too. The one from [Jose] Gimenez v Porto is, in theory, similar to Felipe's one tonight. These are up to the VAR people and the referees themselves.
"We coaches should be focused on improving the team and not stop on these things, which of course have an influence on the game because having one man less is a lot, especially in the first game when we were competing well and nearly winning the game.
"So, that decision made more difficulties for us in the game. Now is the time to be quiet, work together and again, I like how the team accepted its role in the second half and I give them all the credit for this."
"It is not a very different situation to the ones we have gone through in previous years in the Champions League," Simeone added on the team's group-stage struggles. "Lately, we are struggling to go through from the group stages.
"We used to do it much easier before, not reaching the last match with all at stake. It is different lately. So, we have to play a good game against Milan and only be focused on that."
