There was a 69th-minute bust-up between Joe Hart and Tigers substitute Boyd following the latter's appeal for a spot-kick, which resulted in England goalkeeper Hart being shown a yellow card.
Bruce said: "There's a difference between simulation and diving, and trying to get out of the road. That's what Boyd is trying to do - nobody's going to stand there with Joe Hart coming at him.
"I think the referee got it spot-on. But the push in the back (by Fernandinho) looked a penalty."
Bruce was left to rue his side's inability to make the most of their chance to build on last Sunday's FA Cup quarter-final win over Sunderland.
But City showed fighting spirit after they shrugged off the 10th-minute dismissal of captain Vincent Kompany to claim a potentially priceless 2-0 Barclays Premier League win at the KC Stadium.
David Silva's stunning 14th-minute strike and a last-minute effort from Edin Dzeko helped City end a tough week on a high after successive defeats to Wigan and Barcelona had left their dream of an unprecedented quadruple in tatters.
Bruce added: "I think the frustration is we have never had a better chance to beat them. In the end it became one of those frustrating afternoons.
"We know how difficult it is to play against 10 men. We needed the game to go 30 or 40 minutes longer before Silva scored - that gave them something to hang onto.
"It's been a difficult week for Manchester City but I have to say they defended fantastically well.
"We just didn't have the quality to break them down but I have to say City defended very, very well and they scored a wonder goal. Silva's was a fantastic piece of individual skill."
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- Joe Hart