The result saw Villa miss Champions League qualification as they signed off for the season with a defeat.
Emery said: “Today, we lost the opportunity, but we didn’t deserve more.
“We started the match today, poor in our performances, collectively and individually.
“It was the key moment for the sending off of Emiliano Martínez and, of course, after it, we needed to be resilient, we needed to defend, we needed to defend low block, goalkeeper, and believe in our moment to get some attacking actions, or some corners.
“We scored one goal, and normally this goal, if the referee was under his control, this moment, to wait before to whistle this action, I think it was a goal, after VAR. We watched on the TV.
“But we are making mistakes, the players, they are making mistakes and the referees, sometimes they are making mistakes.
“We have to accept it. We lost and we didn’t deserve more.”
We are in Europe
The result leaves Villa with a sixth place finish and Europa League qualification.
Emery also said: “Frustrated today, but we are in the Europa League, we are in Europe.
“Last year in Conference League, this year in Champions League and next year in Europa League.
“To be in Europe is important and being in three years in a row I think is something we are showing our consistency.”