Danny Cowley was convinced MK Dons' winner should not have stood because George Williams was '100 per cent offside' when he deflected it past Josh Vickers.
Williams was on the floor when he flicked a heel at Jordan Bowery's shot to send Dons 2-1 up, despite protests from the Lincoln keeper afterwards.
Lincoln boss Cowley, who watched his side lose their 100 per cent start to the League One campaign, said the linesman made 'an unbelievable decision' in keeping his flag down and allowing the goal to stand.
"If you’re laying down right on the goal-line, there’s a good chance you’ll be offside," he said. "I’ve seen it back, it’s 100 per cent offside, he’s laying still on the floor, it’s categoric.
“It’s an unbelievable decision and I don’t know how he [the linesman] has got it wrong.
“It is what it is and we can’t affect the referee’s decisions. I don’t want to use that as an excuse because it’s not the reason [we lost]. The reason was that we allowed a team that only had 11 touches inside our box to score two goals.
“It’s doesn’t matter how well you played – and that was probably the best we’ve played under me box to box – it means nothing because football is won in both boxes.
“You can’t win games if you don’t defend well. They had just 11 touches in our box in the whole game and still scored two goals.
"We were far too soft in combat in the first half. We didn’t defend our box well enough. When you don’t do that and concede two goals, you give yourself a mountain to climb.
“People can tell us we’re a good team, but you’re not a good team if you concede goals like that."