Aleksandar Mitrovic capitalised on Dunk's error to give the visitors a 2-0 lead before the Seagulls fought back for a draw.
Hughton conceded it was maybe a wrong call to play the defender so soon after recovering from an ankle injury.
"Dunky is a particular type of individual. He rarely misses training, he heals very quickly. Although he hadn't trained with us, he'd done some good running. We were confident with his levels," said Hughton to the Argus.
"He made one (mistake) and he'd be the first to hold his hand up. But that's part and parcel of his education at this level. I thought both him and Shane (Duffy) were up against a very good player in Mitrović, good movement, very strong, and a good experience for both our centre-halves."