'Well were beaten 2-0 at home in the first leg of their qualifier, and there were echoes of last season's defeats by Panathinaikos and Levante in the concession of a late goal.
Kuban's second goal came from a break as they defended a Motherwell corner, much to McCall's annoyance.
"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."
John Sutton hit a post late on, but McCall's side face an uphill task in Russia next week if their European campaign is to continue.
McCall said: "Listen, they were a better side, they were a yard sharper, they created better chances but we were still in the game.
"We came in at half-time maybe fortunate to be 0-0 but they have not been beaten since November and are difficult to break down.
"Our set-pieces weren't great and it would have been nice to see Sutton's chance go in for the fans, they stuck with us all game and that's three 2-0s in a row here.
"The second goal was just so frustrating - even at 1-0 it was an uphill task - but we are still in it. We can still go and defend well and nick a goal on the break or from a set-piece but the second goal is the most frustrating aspect."