The Trotters had kept the home side relatively quiet at the Liberty Stadium until midfielder Ricardo Gardner was sent off for a second bookable offence on Nathan Dyer early in the second half.
The first one came on the stroke of half-time as Gardner and Dyer challenged for the ball in midfield but it was not 100% certain exactly why the Jamaican veteran was booked.
Swansea took advantage of the extra man and immediately scored through Joe Allen from the ensuing free-kick leaving Coyle unhappy as there were a few calls that could have gone his sides way prior to the sending off which ultimately killed Bolton's chances.
"I think the second yellow card, in fairness, Ricardo Gardner has tugged Dyer back. I think we all accept that normally results in a yellow card," he said.
"The first one I wasn't sure about in terms that it was such an innocuous foul. I think it was the first yellow card awarded in the game.
"I think there might have been a couple of challenges where the referee felt he let them go, but that was the first free-kick against him so maybe the referee thought it was persistent fouling, I don't know.
"It felt like two soft yellow cards, but that's the nature of the game now. But having said that, (Neil) Taylor in the first half clearly pulled Mark Davies back and it went unpunished. I think ultimately we want a bit of consistency in the game.
"(At the ) end of the day, it's not for me to sit here and get myself into trouble but there's enough good judges at the game who can make up their own minds as to what transpired."