Portsmouth went down to a late Peterborough strike at Fratton Park in a 3-2 home defeat.
After watching his side dominate the second half, a dejected Cotterill said: "We did enough to win that game - that's for sure. We played well enough and especially in the second half.
"We just got caught with a sucker punch right at the end. Now we've got the feeling that Blackpool had here.
"It's amazing what this game does. We had the euphoria of a last-minute winner on Saturday and then three days later we had to take that.
"We didn't deserve that and if we had taken our chances the game was out of sight."
Cotterill refused to lay the blame on certain players for their costly mistakes.
He added: "Individual errors are very difficult to do anything about. That's what happens - we're human.
"Unfortunately, when goalkeepers make a mistake, it ends up in the back of the net.
"Okay, Erik put it in at the death there, but if he hadn't, maybe someone else would have put it in anyway."
Peterborough boss Darren Ferguson was delighted with their first Championship away win of the season.
He said: "When you score a goal like that in the last minute, there is no way back for the opposition. As it was, it was the last kick of the ball. It was a great victory.
"In the first half I thought we played some really good stuff and caused them all sorts of problems. They changed their shape in the second half and, to be fair, they were on top.
"We dug in, though, and after they equalised, we had to dig in. Then we had a little break at the end to win it."