The hosts slipped to their first home defeat against Ross County in more than four years and are without a win in their last four games.
Changes of system and personnel were trialled by Hughes in an effort to find a way back into the game but Aaron Doran's goal came too late for Inverness to claim a draw.
Inverness were reduced to 10 men in the second half as Ross Draper was dismissed for an elbow on Stuart Kettlewell but Hughes felt his side played the better football throughout the course of the 90 minutes.
He said: "I think we were the better side. They had patches, sucked us in and hurt us on the counter-attack which is disappointing.
"But credit to everyone in terms of effort, they kept on going right until the last minute trying to win the football match.
"We were chopping and changing things to try and get there and maybe we've scored that goal a little bit too late.
"You've got to learn. We're a great, hard-working bunch of lads but we've got to stop beating ourselves. I feel for them but the fundamentals you need out on the football pitch come first and foremost."
Ross County boss Derek Adams praised his side's quick start to the game and felt it was decisive in getting the three points.
The Staggies had been without a win since October 5 and were at risk of being cut adrift in 11th place.
They also brought in new signing Jordan Slew, on loan from Blackburn for the remainder of the season, late on Tuesday night to help bolster their attacking options.
Adams praised his team's quick one-two punch in disposing of Caley Thistle.
"It was important that we started the game well and got the early goal from Scott Boyd," he said.
"Quickly after that Alex Cooper got the second goal and it was great. They didn't really trouble us apart from the goal but they're still a good side and have done well this season.
"They've got players that can hurt you and I thought we did well to keep them at bay today. We haven't been able to get a break and after Inverness hit the post, we got that first goal.
"When you get that first goal in this league it is vitally important to follow it up."