Freddie Sears netted 13 minutes from time for the Tractor Boys, but the home side held out for their third win in four games under Hughton.
McCarthy told reporters: "We have to give Brighton a lot of credit. It was not going to be easy. Brighton played well in the first half and we didn't do well with the goals we conceded.
"We've had one or two players missing through illness and injury and perhaps Brighton have gone up a couple of percent because they are playing us."
Ipswich remain in third place in the Championship table following their defeat, but are just one point adrift of leaders Bournemouth.