The Robins, who had not lost at home since August 2011, went down 1-0 at the County Ground thanks to Lee Cook's goal on the hour.
"The performance was not usual for us," Di Canio told the club's official website.
"I couldn't imagine that this year would be like last, but we have to discover why. Today was the worst performance of the season."
Swindon have the chance to get back to winning ways next Saturday when they travel to Carlisle United.