Villa slipped to a 1-0 loss against Monaco on Tuesday (21.01.25) and the coach is worried that the defeat will cost his team the chance of automatic progression to the last 16 of the competition.
Emery said: "When we are playing games like this, it's important to get three points because I think we lost the opportunity to get in the top eight.
"Today was the key."
Emery has struggled to forge an effective strike partnership between Ollie Watkins and Jhon Duran this season and the pair were unable to find the net against the French side as Villa chased an equaliser.
The Spanish manager said: "The last 20 minutes we played with two strikers and with two strikers we are not being organised with the positioning like I want.
"We have two good strikers. Playing with two strikers is my challenge. Both are very good players but today it didn't work well.
"I made a mistake when I decided to play with two strikers. Until that moment we were more or less controlling the game."
An angry Emery also accused several of his players of "not following the plan" that he set out for them.
He said: "We are being demanding with the players we have and some are not following the plan we are doing. This is the objective I have now, to try to build the team as strong as possible with a mentality we are building."