The Gulls took the lead in Friday's Premier League encounter at the Vitality Stadium through Solly March heading home from Pascal Gross's pinpoint cross just before the hour.
However, two quickfire goals from the Cherries netted by Andrew Surman and Jermain Defoe ensured that Brighton would leave Bournemouth empty-handed.
Hughton told reporters after the game: "[I am] incredibly disappointed. They have a lot of quality and move the ball well but we handled it well for a lot of the game.
"It was two poor goals we conceded. We never looked like conceding before then. I thought it was a really good period for us just before we scored. Up until then, they had a lot of possession but I felt we were always in the game.
"We had some really good phases, phases where we were really comfortable. We need to make sure in the future that once we take the lead we are resilient enough to hold on to it."