CJ Hamilton had Stags ahead only for Toby Stevenson to poke home a loose ball over the line from close range.
“I don’t think the linesman or any of his team have helped him out. But it’s an important decision he’s got wrong,” he said.
“It was a massive claim and I think you can tell by players’ reactions. You get a gut feeling.
“I have seen it afterwards and the kid was offside. If he’d not touched it it wouldn’t have mattered, but he did.”
Otherwise, Flitcroft was delighted with his side.
“We have taken a League One team on today, but not in League Two style,” he said.
“I am gutted we are not in the next round outright, but we’ve still got a chance. We are still in there fighting and that’s important in the Cup.
“It gives our boys the chance to travel down to Charlton, which is a fantastic football club, playing a very good team on a brilliant pitch under the Tuesday night lights.
“We will relish and look forward to that. It’s a team and a club with stature and tradition.”
Flitcroft added: “I told them at the end to be proud of themselves as they have stood man for man on a very important, unique day, representing the club and the town.
“I was absolutely delighted with the way they committed to each other. They put a real shift in and we moved the ball around brilliantly.
“The back three were immaculate – outstanding.
“We don’t know how to get beaten at the moment. We were brave playing three strikers which we knew would give them problems.
“We deserved to be in front at half-time. But no two games of football are ever the same. You never really dominate a team for 90 minutes, let alone a League One club.
“But Bobby only had one save to make and they didn’t really threaten us.”
Hamilton’s pace terrified Charlton all day and, after his storming opening goal, he was hauled down by Bily Clarke when trying to break clear again.
“CJ’s performance was show-stopping. The kid had to nearly assault him to bring him down late on,” he said.
“It was a professional foul and if it’s that blatant we maybe need to alter the rules. It was ridiculous – it was like WWF. He dragged him down.”