The 21-year-old was booked for taking a free-kick too early in the ninth minute of Sunday evening's first-round tie, shortly after his first yellow card, and that left Argyle with a mountain to climb at the Avenue Stadium.
Jake Gosling, on loan from Exeter and released by the Pilgrims at 16, struck the winner just after half-time.
"I understand the decision by the letter of the law that for whatever reason when the referee says that you have to wait for the whistle and then you play it in it's a booking," said Fletcher.
"But Conor says he heard a whistle and he was trying to move the ball back. To lose a man like that so early in the game made it a tough game for us.
"We know Dorchester are a good side and it was a case of making sure that we were right mentally. But I don't think that we had the right quality for decision-making in the second half and we didn't really get to where we wanted to be."