Flanagan was as angry as any coach in a post-match press conference this season on Saturday night, taking particular aim at two calls from the final minutes of the 20-18 defeat in Homebush.
"I was really proud of the effort they put in and the way they played, but the game was taken away from us from I believe wrong decisions," the Dragons coach said.
Flanagan was incensed that the Bulldogs used their captain's challenge to earn a penalty with five minutes left after the bunker ruled Luciano Leilua had interfered in the ruck as Jacob Kiraz played the ball.
The coach accused Kiraz of ball-planting, an illegal move when a player puts the ball on the ground and attempts to play it without regaining their footing.
"The Luciano Leilua decision was outrageous," Flanagan said.
"He's got to get to his feet before he plants the ball.
"You can't be falling sideways. You can't ball-plant ... but tonight we ball-planted and we lost the game because of it."
As the Bulldogs attacked the line on the back of their penalty, Flanagan thought Viliame Kikau batted the ball into Tyrell Sloan as he attempted a quick pass on the left edge.
But the possible knock-on was missed and the Bulldogs continued to attack the line, with Lachlan Galvin throwing the match-winning pass for Jethro Rinakama to score moments later.
"Kikau passes the ball, hit Sloan and goes forward, so in the collision that's a knock-on. Ever since 100 years, that's a knock-on and that was at the 78-minute mark," he said.
The Saints are set to finish the weekend three wins behind eighth spot, their NRL finals hopes now relying on mathematical possibilities.
To finish the season with a winning record, they must claim victory in all of their last seven games - and they face Penrith, Canberra, Cronulla and the Warriors in that stretch.
"They're trying so hard," Flanagan said.
"They're a good side the Bulldogs, they compete hard, but it was some decisions tonight that cost us two competition points and could cost us an opportunity to play semi-finals."
Flanagan confirmed he would seek clarity from the NRL about the decisions.
"I'll go through those channels, but in the end we don't get these two competition points," he said.
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