The 39-year-old said that Boyeson only got one decision right, and that was to award the Royals a penalty when David Wheater handled inside the area.
"They got that penalty and that was the only decision that the referee got right," PA quotes Freedman as saying.
"I've seen some blatant penalties [today] and I won't duck any questions. I've got no complaints with David Wheater's - but it wasn't just the penalty decisions.
"I felt that the flow of the game kept on getting broken up when two really good teams were playing end-to-end football. We can't control that, we can only control how we play."