The Seagulls were unable to show their best at Vicarage Road, and Jones admits that they failed to trouble their opponents.
"We're disappointed [with the result], as a team, as a group. We didn't start too badly, we just conceded bad goals at bad times," Jones told the club's official website.
"The first came slightly against the run of play and that knocked the wind out of us a little bit.
"We huffed and puffed after that without really taking the game to them, then the second goal came at a bad time as well, and salt was rubbed into the wounds with the disallowed goal as well."
Brighton are ninth in the Championship.