The stats back up McInnes' anger. Rangers had just over 46% possession during the 120 minutes in the Czech Republic, and just one shot on target.
They won fewer than 70% of their 16 tackles and committed 17 fouls.
"I can't accept, and we shouldn't accept, losing individual battles, duels, second balls, not winning enough tackles and just getting the momentum of the game going our way," the former Hearts manager added.
"I thought we looked young, inexperienced at times. We're trying to make some signings to help with that side of it but we need to do so much more as a team.
"We got what we deserved. If we'd won on penalties we would have taken it, of course, but it would only have covered over the cracks.
"I'm mortified with the performance. I know you can lose games of football but we should have enough in the building to take care of that tonight."
Rangers had won their two previous games - a 5-1 win over St Mirren in the League Cup and the 1-0 victory against Jablonec at Ibrox - after drawing at Dundee United and losing at home to Hibernian in their opening two Premiership matches.
But McInnes feels this latest result may set them back.
"We went into this game scrambling for some sort of confidence, some positivity," he said. "But I just thought the team that deserved to go through went through tonight and that's hard for me to take."

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