Sancho was sent on on 29 minutes for the injured Emi Buendia, though lasted only an hour before being replaced by Ross Barkley.
Sancho snubbed Barkley when crossing the touchline ahead of also ignoring Emery as he stormed away to the dugout.
Afterwards, Emery explained: "It was not easy, firstly, after Sancho played 60 minutes against Go Ahead (in the Europa League on Thursday). He is getting fit, but not enough.
"I planned as well with him to play him in the second half, but after the injury to Buendia, I decided to get him on the field as best as possible to get minutes and fitness, using his skills and qualities.
"His impact was good, but I knew before that it was my plan was to sub him, and I did it before with Morgan Rogers and Emi Buendia.
"It was not a punishment, it was a plan - he played 45 minutes. The other sub players were ready. Malen, Maatsen and Barkley were all very good."
Sancho is on-loan at Villa from Manchester United, where he is off contract next summer.