Kei Kamara's first-half strike and a wonder goal from left-back George Friend put Boro in the driving seat but Forest salvaged a point when Matt Derbyshire and Darius Henderson found the net in the second period.
Mowbray was disappointed to see his side squander their lead but he was even more frustrated by some of the decisions made by referee Phil Dowd.
"I thought he (Dowd) got quite a bit wrong," he said. "It's not an easy job, the modern-day referee. But he gets paid for making decisions and he made them."
Forest were awarded a first-half spot-kick for a foul by Rhys Williams on Radoslaw Majewski, only for Andy Reid to see his kick saved by Jason Steele. Mowbray took umbrage at Dowd's decision.
"What I don't like about officialdom at times is the over-dramatic nature of the decision," Mowbray added.
"He saw where the ball went - and I know Williams won the ball pretty cleanly - but the dramatic nature of him standing there for three, maybe four seconds before pointing to the spot in dramatic fashion. I don't think there's any need for it."
Mowbray also believed his side should have won a late penalty of their own when Marvin Emnes was brought down in the box, adding: "I'm sure Billy (Davies) will be just as aggrieved as I am about the refereeing decisions.
"I cannot believe we were not given a penalty decision near the end - the lad has practically rugby-tackled around the waist and pulled him to the ground. It is unbelievable."
The Boro boss was, though, pleased with his side's display despite the end result.
He said: "They never really felt threatened. Yes they put a lot of balls in the box but (Jonathan) Woodgate and Williams headed a lot of balls out and stood out well, while we looked a threat on the break, highlighted by both of our goals.
"They nullified our passing game, but we stood up to the test pretty well."