Luciano Becchio's 65th-minute penalty proved decisive as Freedman's side failed to convert their chances in a dull New Year's Day encounter.
The Trotters boss was also frustrated by the decision not to award a spot-kick for a foul on substitute David Ngog, which left his team with just one win from their last nine away games.
He said: "It was a game we should have won because we created most of the chances. Our game plan is working but our defence is letting us down and that is what happened here.
"We looked comfortable and in control for most of the match but Leeds never gave up and I am sure their manager is very happy with the win."
Freedman added: "The referees and their assistants are part-time, so it is not their fault. They don't train all week and they don't get help. They don't get coached or mentored.
"There should be a more professional approach because there is so much at stake."