The Seagulls arrived at Goodison Park off the back of a seven-match unbeaten streak across all competitions - including three wins in a row - but they were well beaten by the Toffees on Merseyside.
The result saw Brighton fall back into the bottom half of the table, and Hughton acknowledged that they did not deserve anything out of the game.
"We fell well below the standards we've set and the level we needed, at a place like Everton to get a result," Hughton told BBC Sport.
"We've been on a very good run and came in to the game with a lot of confidence. We restricted them to minimal chances going into half time. Once the first goal goes in it lifts the crowd here and it becomes very difficult.
"In that last period they were able to raise their game, they have a lot of offensive options in their squad. You want a reaction from the team. Generally we've been in most games but this is not a good one for us today particularly with the run we've been on."
Brighton remain seven points clear of the relegation zone, but they must still face all of the current top four before the end of the season.