"They were the better side throughout," Cotterill said. "We haven't got any grumbles, we haven't got any complaints.
"They were better than us today. We can't make any excuses. They were a better team and beat us fair and square.
"We shouldn't be shocked or surprised by today's result. Disappointed, of course. But they were the better team. Full stop. They deserved their win."
The home side, who had not won at Home Park since the beginning of October, were full value for their win.
They amassed 15 shots on target to the visitors' none and had two apparently cast-iron penalty appeals turned down be referee Lee Probert before Wotton eventually made the breakthrough.
Wotton, the only survivor of the last game between the two clubs, when Burnley won to relegate Argyle to the old Third Division, dedicated his winning strike to his young son, Alfie, who has been ill recently.
He said: "It was probably one of my best penalties. The keeper was nowhere near it. The ball hit the net before he even moved.
"If we didn't get three points today, the boys would have been low because we put so much into that game. We had numerous chances. We deserved three points and we needed three points."