Welbeck struck a double in their 3-3 draw with FC Basle after returning from a major hamstring injury.
Ferguson did praise Welbeck's contribution, saying the 20-year-old 'did very well' in the first half but had tired in the second.
And Welbeck himself admitted it "felt like a defeat", despite Ashley Young's last-minute point-saver.
"We should have put the game away," said Welbeck. "It's just not like us. I'm over the moon with two goals, but it's a team game and I'm disappointed with the result."