Wanderers went behind in the ninth minute after Andy Keogh won a penalty and delicately placed the ball past Adam Bogdan, but Keith Andrews managed to equalise from another spot-kick later in the first half after Chung-Yong Lee was brought down in the box.
The Trotters were then on the front foot in the second half but failed to take the lead although Freedman was happy with how his men performed.
Freedman said: "The players showed tremendous effort throughout that performance and that was the most pleasing thing for me.
"If I have any criticisms we were a bit wasteful and our decision making wasn't good enough.
"I think when the goal went against us made us up the tempo and I felt in the second half we gave everything we had.
"Should we have got them towards the end? Possibly through our attacking and opportunities but it wasn't to be today."
Former Watford frontman Marvin Sordell was subjected to constant abuse from the Millwall fans but Freedman insisted it did not affect his decision to bring him off the bench.
He said: "It was a difficult one for him and he was in a low place when I first came here because he's a young guy who moved here from London and he's still settling in.
"I know the Millwall fans and they used to give me a lot of stick and the stick he was getting from them wasn't on my mind when I subbed him on."