The Bluebirds had gone ahead against Maurizio Sarri's side through a fine goal from Victor Camarasa, mere moments after returning to the field after half time.
Cardiff looked to be hanging on for three points, but an 84th-minute header from Cesar Azpilicueta, who was in an offside position, levelled matters before Ruben Loftus-Cheek nodded home the winner in added time.
Warnock could not hide his frustration with officials after the match, labelling them 'the worst in the world'. And while Hughton understands his counterpart's grief, he doesn't feel quite as strongly as the 70-year-old.
“I can certainly understand Neil's frustration after a game where there were some decisions that went against his team,” the Albion boss said. “I can understand his feelings and his emotions.
“We are also a team that has been on the end of some poor decisions that have gone against us, but that's part and parcel of the games.
“I certainly feel that we have a good overall standard of refereeing here but VAR will come in next season and I think that will change the game.
“At the moment, though, there are still going to be decisions that are going to be tough to take, particularly with the number of cameras now that we have at stadiums and the amount of footage that's being shown.”
A win for Cardiff would have given the Welsh side greater hope of surviving a relegation battle at the foot of the Premier League but would also have put Brighton – who are only five points ahead – in danger of being caught by Warnock's side.
With that in mind and just eight league matches remaining, Hughton has urged his team to work harder than the rest of the lower-level teams rather than hoping for slip-ups from other relegation-threatened sides.
“I suppose the first priority for us is to make sure that our own results are good enough, that we don't have to rely on others,” he said.
“But as soon as our result is finished you want the other teams around you to have not done well.
“We are amongst a group of teams that are fighting every game and we've got to be fighting, if anything, harder than the rest of them.”