The visitors took the lead through Richard Duffy, but strikes from James Coppinger and John Marquis either side of the break put Donny in the lead.
Notts thought they had equalised when Haydn Hollis headed home in the second half, but the flag went up to rule the goal out, much to the bemusement of the travelling contingent.
Andy Williams added a third for the hosts in stoppage time as Notts sent goalkeeper Adam Collin forward, and Nolan was at a loss to explain why Hollis's goal was snuffed out.
"I still don't know why the goal wasn't given," he told the Nottingham Post. "It's the most disappointed I have been with the officials since I've been in management. I thought they were poor from start to finish.
"Why it was given for a free-kick I will never know. I've had a look at the video and I still don't see. I spoke to the referee briefly after the game and told him what I thought.
"It was disappointing because I thought the lads were fantastic."
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