The Seagulls failed to register a single shot on target at Vicarage Road as Watford eased to all three points courtesy of a brace from Roberto Pereyra.
Brazilian full-back Bernardo was the only one of Brighton's 10 summer signings to be named in the starting lineup, and Hughton admitted that he was concerned by the manner of his side's defeat.
"I have no complaints with the result. I thought we lost to the better side in most departments," he told reporters.
"It's a concern. We can't have any complaints about new players settling in because, apart from Bernardo, it was last season's team. There are no excuses, the players who played today know the system well.
"We don't go into any game thinking we have to work less hard to get a result, but this was our first opportunity, especially away from home, to win a game and we didn't."
Four of Brighton's next six matches come against teams who finished in last season's top four.