Emery's side waved goodbye to the competition after playing out a goalless draw at Atletico Madrid on Thursday.
The visitors were denied a late penalty that could have made the difference.
Valencia substitute Nikola Zigic had his jersey torn after he was pulled back Atletico defender Juanito while he was going for a close-range header four minutes from time.
However, the referee didn't point at the spot.
"You have all seen it, the television doesn't lie. When you decide to have extra officials it is so this type of incident doesn't happen," Emery was quoted as saying in Spanish media on Friday.
UEFA is applying a new five-official system to deter recurrent refereeing mistakes, with two additional assistants near the penalty areas to help the referee make the right decision.
"We believe the referee didn't have the strength of character (to give the decision), neither did his assistants," Emery added.
"When they see the incident they will be ashamed."