Former Iron favourite Matt Sparrow threatened to return to haunt his old club when he fired Crawley in front in the 48th minute with his first goal since joining them in January.
But the hosts came roaring back with goals from Jimmy Ryan and centre-back Niall Canavan to snatch a 2-1 victory.
Crawley's hopes of making the play-offs appear to be faltering after only one win in their last five games.
"It is very frustrating," said Barker. "We have brought in a lot of new faces and we have a very young squad who going to need time to gel. But that has been made very difficult by a very stop-start fixture list that we have had.
"We have a very disappointed dressing room in there. They know they have let themselves down with the way they have played.
"I let them have their say first after the game - and I was pleased with their reaction.
"Without playing particularly well, this was a game we could have won after going in front early in the second half. We are going to have to learn how to win games like this - and quickly.
"But the margins are so fine between success and failure. Five minutes before Scunthorpe got their winner, we came so close ourselves when Jamie Proctor, at full stretch, has hit the crossbar.
"But what disappointed me most was the way we conceded the two goals that gave Scunthorpe the three points. We have to learn from that and move on, but to be leaving here with nothing is very disappointing."