The visitors caused Watford a host of problems in the first half and former Hornets striker Marvin Sordell gave his side the lead from a penalty in the 32nd minute following Daniel Pudil's foul on Sam Ricketts.
The home side responded four minutes later when on-loan Udinese striker Matej Vydra eased past Bolton's defence to stroke home from 10 yards out. The winner arrived 20 minutes from time when Almen Abdi stroked the ball into the bottom corner of Adam Bogdan's goal.
Freedman said: "I felt our game plan was working very well throughout the match. I felt we contained a very good Watford side to very limited opportunities.
"I felt we controlled the game through our passing and our movement, our regains were very good.
"I didn't feel we put enough pressure on their goal throughout the game and it's disappointing that we conceded a goal right after we got the goal.
"That was probably the most disappointing thing, it changed the crowd and it changed the game a little bit in the second half.
"In the second half it was poised and very, very even but right now we are going through a very difficult moment and we've got to believe in ourselves - that's what missing."