The hosts saw James Chester sent off after just 14 minutes, though referee Jon Moss had little choice in making that call as the defender denied a goalscoring opportunity following a defensive mix-up.
Hull responded manfully and took the lead through Nikica Jelavic just before half-time, only for Stoke to salvage a point when Ryan Shawcross bundled in a late leveller.
But that goal came from a throw that clearly should have gone to Hull, leaving Bruce angry.
"Given the circumstances, I think you would accept a point after you're down to 10 men after 15 minutes," said Bruce.
"However, we feel there was an injustice, of course, and when you see it, how blatant it is, I just can't understand how the three officials can't get together and make that decision right.
"The whole of the crowd knew it was ours and their player ran away and didn't even go to take the throw-in, so surely that's an indication to the referee or the linesman to say 'hang on a minute, it must have hit him'.
"And it wasn't just a slight deflection either - I think everyone in the ground must have seen it, except for the three officials. And the consequence of it was, that because we thought it was our throw, we weren't set up the way we should be.
"It's difficult to take and difficult for the players, because after their exertions in midweek and playing with 10 men for 75 minutes, the determination to succeed was manful to say the least.
"I got into trouble twice last year and vowed I wouldn't give the FA any more money, but we've already had two awful decisions. Last week [against QPR] it didn't count when he had a penalty go against us, but let's give the referee a hand as the fourth official has a monitor next to him.
"But I expect three officials to get it right because it wasn't just a slight ricochet, the ball completely changed direction, and who knows where those two points might have taken us, as the decision has cost us victory."
