The Dons won this fourth round replay 2-1 at Fir Park, with Rory Fallon and Joe Shaughnessy netting for the visitors early in the second half, before Michael Higdon fired a last-gasp consolation from the penalty spot.
McCall said: "I'm disappointed to be out of the cup.
"It wasn't to be. Second half they were better, there's no doubt about that.
"We couldn't find a way past them. I thought Mark Reynolds was outstanding at centre-back for them.
"We've now got to go on and try to clinch a European place via the league."