Jermaine Beckford missed a late spot-kick for Freedman's men, leaving new Middlesbrough boss Aitor Karanka to celebrate a 1-0 victory in his first home game in charge thanks to Grant Leadbitter slotting home a penalty of his own after 82 minutes.
"It was hard for the boys because they worked very hard in that game and in the second half especially we had a lot of possession and created some good chances," said Freedman.
"And defensively we were very good. We restricted them to very few chances and our keeper has barely had a save to make. It stings a bit to concede from a penalty and obviously it stings to miss one too.
"But we played well. I think we played well enough if not to win, certainly not to lose the game.
"Now it is about how the team react. It is the first defeat after a long run of good results and the spirits have been high.
"But I'm confident that they will react well. We have been in great form and I'm sure there will be a positive reaction."
Bolton last week