The Blues got themselves level after being 2-0 down and looked to have done enough to draw their fourth game out of four.
But nobody told Sutton as substitute Kieron Cadogan nipped in to snatch their three points back. It took them to the top of the Vanarama National League.
But McCarthy knows that, despite not yet winning, there are a lot of plus points to take away from the first two and a half weeks of their season.
He said: "I feel for everyone associated with the club. My staff, the players and the supporters because everyone was fully behind what we were doing today.
"They are the new league leaders and they are up there because they are strong, direct and difficult to play against.
"At 2-0 down we did fantastically well to get ourselves back in the game and then back level.
"For us to get ourselves to 2-2 and then for that to happen in the last few minutes, well it's killed us. It hurts.
"But it's gone. We have got to turn our focus to Aldershot now and we know that will be tough because they are very strong at home.
"The downside is we have let in three goals, but the reaction and the response was first class. I want to thank the fans.
"We are on a tough run of fixtures and it's a difficult September too so it doesn't get any easier," the manager told the ChesterFCTV channel.
"But if we can keep picking up on how the supporters are helping the team, there will be a lot of points to be picked up."