The Steelmen conceded to Ivelin Popov in the 52nd minute before allowing the Bulgarian attacker to score again with just over ten minutes remaining and manager Stuart McCall was bitterly disappointed as the performance reminded him of their qualifying campaign last season.
"We got to 74, 75 minutes and the plan was to go 4-4-2 and launch some balls in," McCall said.
"But the second goal - I saw it coming, as soon as it came out and we played the wrong pass.
"It was deja vu - exactly the same as last season. We talked about it all week and by the looks of that we didn't learn. That's most disappointing aspect."
Motherwell will now look to arrest that two-goal deficit when they head to Krasnodar next Thursday.