Marvin Sordell had given Bolton the lead against his old club, but the Hornets turned the game around with goals from Matej Vydra and Almen Abdi.
Freedman admits he is happy with much of his team's play, but he is looking for them to start posing more of a threat in the final third of the pitch.
"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," Freedman said.
"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."