The defeat effectively ended the Dragons' slim finals hopes with Flanagan angry a second-half try to Warriors centre Adam Pompey was awarded as the hosts recovered from a 10-0 deficit in Auckland.
Trailing 10-4, Pompey crossed in the 63rd minute after a backline play where second-rower Marata Niukore ran a decoy and knocked Dragons five-eighth Lyhkan King-Togia over on his outside shoulder.
King-Togia threw his arms up in protest and Dragons captain Clint Gutherson complained to the referee about Niukore's action.
In Fox League commentary Greg Alexander said "there might be some questions asked about this one".
Niukore threw his head back and Alexander added "he's got a problem," but the Bunker ruled King-Togia had milked it.
Last week, North Queensland had a try to Jake Clifford correctly disallowed in the final minute when Jeremiah Nanai took out Mitchell Moses in a similar circumstance as Parramatta escaped with a 19-18 win.
Unprompted, Flanagan raised the inconsistency in Friday night's post-match press conference at Go Media Stadium.
"I know they haven't asked a question, but I'm going to give you an answer," the premiership-winning coach said.
"You know, it's really tough for us that what was an obstruction last week isn't an obstruction this week.
"I've been involved, started playing footy when I was four years old, I don't know the rules anymore.
"As I said, last week it was obstruction. This week it's not.
"The boys asked out in the field numerous times. They just got shooed away, so that's frustrating."
Compounding the Dragons' woes was losing three forwards in the first half to concussion.
Flanagan's side had to activate 18th man Tyrell Sloan after back-rowers Hamish Stewart and Jack De Belin fell victim to some friendly fire, both ruled out with category-one concussions after clashing heads trying to bring down Warriors enforcer James Fisher-Harris.
Then interchange forward Hame Sele also failed a HIA following a 29th-minute head knock.
"It's tough," Flanagan said.
"But we're a tough club and this is a tough unit, a connected unit, and we'll fight really hard for the next three weeks."
The Dragons face South Sydney, Manly and Penrith to finish their campaign and would need to win all three games handsomely and hope the Sydney Roosters and Brisbane lose all three of their remaining games to have any hope of squeezing into the finals.
While the injury-hit Warriors returned to the top four with the victory, the win came at a big price.
Prop Jackson Ford was charged with a grade-one crusher tackle on Dragons winger Corey Allan and been hit with a three-match ban.
One extra game's suspension would be added should he contest the charge and lose at the judiciary.
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