Wasps prop McIntyre was adjudged by referee Dave Pearson to have not bound properly in the dying seconds as Wasps pressed to end their poor run of results just five metres short of the Exeter line.
The decision ended Wasps' hopes of salvaging anything from the game and catapulted the troubled club further into the relegation mire with an eighth successive league defeat.
Wasps director of rugby Young said: "I've got to be careful with what I say otherwise I'll be dragged over the coals.
"There must have been only two people in the whole stadium that felt that it was a penalty to them.
"I thought it was a very poor decision and that's lost us the game in the end.
"I'm not saying we were dominant for 80 minutes because we weren't but we did enough in the second half to win the game.
"We were given two penalties but then we were penalised for trying to play on for two or three phases, then it was advantage over when it clearly wasn't.
"We've been told they don't want us to just chuck the ball away and take the penalty - they want us to be positive and try to play, which we did.
"In such a tight game, we had two kickable penalties taken away from us."
Five Ignacio Mieres penalties helped Exeter to rise to fourth in the table, while Newcastle's win over London Irish has reduced the gap between the Falcons and Wasps at the bottom to just six points.
Nick Robinson replied with four kicks of his own for the hosts.
Exeter head coach Rob Baxter said: "The scrum seemed to go from a stage where we looked the dominant side to a stage where the bodies changed and we became a bit penalty-ridden.
"There seemed to be a fair bit of input from the touch judges on binding - we won the penalty at the end for the Wasps tighthead not binding and he wasn't binding.
"You get some pens and you lose some pens in that kind of battle and you take what you get.
"It was obvious we weren't going to be able to play much rugby with the way the conditions were and we had to change things.
"We had to create pressure through keeping the ball and we didn't do that very well in the first five minutes where we gave away cheap penalties, but it showed us what not to do and we didn't do that much for the rest of the game."
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