The Tigers boss felt Gareth Barry should have been flagged offside for the first goal - credited to Kevin Mirallas although there was a hint of a touch from the England midfielder - and then sent off for a "horror" tackle on Sone Aluko.
To add to the insult Barry had already escaped with a high tackle on Danny Graham which resulted in the Hull striker being carried off on a stretcher with a knee injury.
Graham's replacement Yannick Sagbo equalised on the half-hour only for Steven Pienaar to return from a six-week absence with a hamstring injury to score with his first touch 30 seconds after coming off the bench.
"There is no-one more of an admirer than I of Gareth Barry, he is a really great player, but he has nudged the first (goal) and changed the course of the ball standing a yard offside," said Bruce.
"We've had one or two go our way but the big ones today have not gone our way.
"The linesman has got to flag - he (Barry) is a yard offside and he touches it, I am 100 per cent certain of it and he runs away like he's touched it.
"I'm not saying it's the referee's fault but surely the linesman has to flag for offside even if he hasn't touched it as he has stepped over it so he has to be interfering with play."
Turning to referee Neil Swarbrick's leniancy towards Barry, Bruce added: "It was bad enough the challenge on Danny Graham but when you see the one on Aluko, it is the stuff of horror.
"Danny has a knee injury and we're not so sure how it is. That challenge is worthy of probably a yellow card and the challenge on Aluko is horrific.
"He is lucky to get away with it as it's over the ball, just below his knee - a horror challenge."
Everton manager Roberto Martinez diplomatically swerved questions over the disputed first goal and saw Barry's tackles differently.
"I think there were a few challenges due to the conditions - the rain made the pitch quicker and faster - and I thought the referee understood," said the Spaniard.
"I think Gareth gets the ball and then it slips away and I thought the decision to give a yellow card was right considering that was the level given to other challenges in the game."
On the goal he added: "I haven't seen it so I can't really comment.
"I think the way it was understood (it was Mirallas' goal) but I'm going to check. I wouldn't like to gamble on that one."
Martinez was far happier talking about Pienaar's first appearance since August 31.
The South African was not expected to return until next week but the manager changed his mind a couple of days ago.
"Thursday's session he looked really sharp and he finished so clinically I felt he was not ready for 90 minutes but we had to have him around the team," he said.
"First touch and back of the net is quite an impact.
"Steven Pienaar brings something really special to our side, for many reasons - firstly the understanding he has with Leighton Baines and also the way he can find space.
"We knew he couldn't play 90 minutes but the impact he had in the game was terrific.
"It was important for us to have that little bit of magic to get that second goal."