Interim Owls boss Steve Agnew has questioned the fairness of the use of video assistant referee (VAR) system in the FA Cup this season.
VAR is only in place at Premier League grounds in the competition and it caused controversy over the weekend.
Everton boss Marco Silva was left furious with the rules after his side lost 3-2 at Millwall. Silva claimed "it did not make sense" that VAR was unavailable in the tie, with Jake Cooper appearing to score an equaliser for the Championship team with his arm.
In stark contrast, Wednesday were left cursing the availability of VAR in their defeat at Chelsea on Sunday evening. Referee Andre Marriner awarded the Owls a 22nd minute penalty after Joey Pelupessy went down under a challenge from Ethan Ampadu.
But the decision was swiftly overturned by VAR after TV replays showed Ampaduslid in and won the ball before being kicked by the Wednesday midfielder.
Moments later, Marriner pointed to the sport after Blues academy graduate Sam Hutchinson brought down Cesar Azpilicueta. The call was reviewed, but deemed right this time and Willian coolly fired the cup holders in front.
"It does seem a bit strange (it is not in use in every game) because an FA Cup tie between Millwall and Everton has the same importance as Chelsea v Sheffield Wednesday," Agnew told The Star.
Agnew, who is set to hand over the reins to incoming manager Steve Bruce, accepts the VAR decisions were spot on.
"You can't argue with the fact that they have got the decisions correct." he said. "It was just a little bit of a mystery to me why we were not awarded a corner.
"If Joey Pelupessy has touched the ball on to their defender, then it has to be a corner and that's the disappointment. Why didn't he (the referee) give that decision?
"Within two minutes, they had a penalty at the other end."
After Wednesday's penalty was rescinded, play restarted with a dropped ball. A drop ball is awarded if a penalty decision is reversed according to VAR rules.