Hull's chances of success were given an early boost when Vincent Kompany was sent off for bringing down Nikica Jelavic, but they fell behind just three minutes later as David Silva curled in a wonderful shot.
Despite their numerical advantage, the Tigers carved out few chances to equalise and had appeals for a penalty waved away when George Boyd went round Joe Hart before going to ground, with replays showing there to be no contact.
Edin Dzeko added a late second for Man City and Bruce admitted after the final whistle he would be speaking to Boyd about the Hart incident.
"I will have a word with George about when he's gone round (Hart)," Bruce said. "In that situation players are waiting for it and when you're at full tilt, you should be waiting to get out of the way.
"I'll have a word with George on Monday and see what his thoughts are."
The defeat leaves Hull only five points clear of the relegation zone and Bruce was frustrated to miss an opportunity to get something against one of the title contenders.
He added: "I think the turning point was the goal Silva got. Had we gone 15 or 20 minutes without them scoring then it might have been a different situation.
"We were continually chasing the game and when you do that against a quality side who are defending deep with 10 men then you huff and puff and get frustrated. It was a difficult afternoon."