Former Northern Ireland midfielder Mark Hughes grabbed the only goal of the game as Bees boss Lawrie Sanchez, a famous cup giantkiller of years gone by, put one over his old Wimbledon pal Cotterill.
"We got what we deserved and got beaten," Cotterill told Pompey's official website.
"We worked so hard to draw at Middlesbrough on Saturday, but we didn't look as if we were there from the off against Barnet.
"We didn't look like we wanted to get hurt - that's why we didn't pick up any second balls or win enough challenges.
"There were too many people passing the buck and not enough of them passing the ball.
"I'm not best pleased and the players know my thoughts. Only if we do well on Saturday against Brighton and Reading next Tuesday will we look back on this and maybe think being out of the Carling Cup is a blessing.
"You always want a run in the cup, but we had three games in it last year, and it does end up taking its toll.
"It's a great night for Barnet. They did well and we've got to give them credit.
"We're really disappointed, but it's not the end of the world and we'll be ready for Brighton on Saturday for what will be a completely different game."
Cotterill's stretched resources were illustrated again after he could name only two outfield substitutes for the match.
"It would have been nice to have changed it around from Middlesbrough and brought different faces in, but we don't have that luxury with the size of our squad."