Although he conceded United were worthy of their point he was upset by the way it was scored, feeling keeper Dean Brill was fouled in the lead-up to Farid El Alagui's equaliser.
Youngster Ryan Christie had given Caley an early lead but they were unable to hold on as the visitors dominated the second period.
"The first 30 minutes we were good. We controlled the tempo, showed good ball retention and scored a good goal," Hughes said.
"However, it was all Dundee United in the second half. Did they deserve something from the game? Yes, 100 per cent.
"But the way they got the goal was disappointing as I thought we should have had a free-kick as the boy jumped into Dean Brill. For me, that's a free-kick."
Dundee United assistant boss Simon Donnelly was pleased with his side's second-half performance and said their early struggles were not down to having one eye on the forthcoming Scottish Cup final.
He added: "We were quite flat first half. Inverness were winning the second balls and we were reacting rather than anticipating.
"In saying that, we had two or three great chances. We had a couple of one-on-one's where you would be expecting us to score.
"I really don't believe the boys would have been thinking about the Scottish Cup final. We were asked after we lost to St Johnstone recently if focus had been lost because of that, but then we go and beat Motherwell 5-1.
"The frustrating thing for us in that we go from that type of performance to what we showed in the first half against Inverness."