The Gunners lost the match 3-2 on penalties after normal time ended 2-2.
Speaking after the match, Emery said: "Ainsley started the warm-up but he felt some muscular pain.
"We decided not to risk him. Our objective was not to take injuries so we decided he didn't play
"Mustafi's the same. He had some muscular pain.
"Yes [it's a calf problem for Ainsley]. "I hope it's not more and not a big injury. But he was starting to feel pain in his calf and we decided it was better for him not to play."