Sol Bamba netted a 90th-minute goal to give the Bluebirds their second Premier League win of the season, but replays showed that the Cardiff City defender was in an offside position during what was a goalmouth scramble.
Albion felt the goal which saw the hosts cap a dramatic turnaround should have been disallowed and were also unhappy with Dale Stephens' first-half red card with the scores level at 1-1.
The midfielder caught Greg Cunningham on the shin with his follow through after winning the ball and was shown a straight red card.
That came after Lewis Dunk headed Albion ahead after six minutes, before Callum Paterson headed Cardiff level after a fortuitous bounce off Gaetan Bong.
Here's what Hughton had to say at full-time...
On Dale Stephens' red card
"Firstly what I would say is that Dale has given the referee a decision to make. In his defence, I have seen players go in with a straight leg or studs raised early. When Dale raises his foot and the studs are showing it is late in the challenge.
"I don't think there is much contact with the player and I think on other occasions the referee would not have given it. On some occasions a referee gives it, on other occasions they don't.
"They are the balances. Unfortunately for us, we had a referee that gave it today, but for that sort of challenges, I do believe some would have given it and some would not."
Sol Bamba's winner
"I do think it looked like he might have been offside. I am talking about the second one, he is offside on the second one.
"I accept referees have difficult decisions to make. There was a style of play where there are always going to be particular bits of contact. When we were down to ten men we knew that Cardiff were going to get balls into our half and it would be a competitive game.
"I understand they have decisions to make, but what you want them to do is make the big decisions correctly.
"I understand with the sending off that some would give it and some wouldn't, but the winning goal he is offside. For me, that is not a difficult decision to make. We have a linesman in a good position when the ball comes back in.
"For me, I am more angry with the second decision than the first one."
Sol Bamba not being booked for removing his shirt off in celebrating his winner
"I will avoid that one. In the balance of the game where a decision could have gone either way in the sending off and a decision should have gone our way in the goal, that's more of my thoughts at the moment."