Flood pulled a hamstring, while Hayes was stretchered off after a sickening clash of heads with Wasps defender Daryll Meggatt.
McInnes, whose side won the shoot-out 6-5 after the game finished goalless, said: "Josh Magennis reported with a shoulder injury and we were already missing Barry Robson, and that's before the injuries to Jonny and Willo.
"We were battered and bruised a wee bit, but we got through the tie and I'm delighted with every single one of my players."
"Hopefully the two boys aren't too seriously hurt. Willo's hamstring went, and with Jonny I don't think it's anything too serious but obviously it's serious enough."