The former Sunderland manager felt both a penalty given against his side that was later missed, along with a foul given that led to the winner for Barnsley were poor decisions, which cost Town at least a point.
Speaking in the post match press conference Keane said: "I couldn't understand what the penalty was given for. None of their players appealed for it and I didn't agree with the free-kick against Tommy Smith that led to their second goal.
"He's won the header and then they have taken the kick 10 yards further forward. That said we should have dealt with it. A minute before that, we had one kicked off the line and you go from almost winning it to losing in with the last kick of the game.
"We had the better of the chances and deserved more than we got but that's the way it's going for us at the moment."
Town have now took just five points from their opening 11 games of the season leaving them bottom of the pile and are a further 5 points away from pulling themselves out of the Championship drop zone in a season where they were expected to be challenging for the automatic promotion places.