Substitute Andreas Weimann hit a second-half brace to turn the tie around after Brent Holman had cancelled out Steve Morison's opener.
Christian Benteke cracked in a fourth during stoppage time as Paul Lambert got one over on his former club.
Hughton, who turned 54 on the day of the match, said: "We needed to make sure we held onto our 1-0 lead longer, and then at the start of the second half, we had a great chance and if that goes in then possibly it is a different story.
"Villa are a good footballing side and they were more clinical than us.
"It is really disappointing because we had been on a good run.
"We have to take it on the chin and now need to make sure we can get back on track for Saturday against Wigan."