Pilgrims boss Ian Foster was furious with referee James Linington after seeing his side take the lead thanks to Morgan Whittaker's tenth-minute opener before conceding two second-half goals.
Josh Sargent struck in the 67th minute before Ash Phillips scored an own-goal seven minutes later.
Foster was critical of Linington's decision not to award a penalty to Plymouth when Alfie Devine went down under a challenge from keeper Angus Gunn, while the official's insistence that Lewis Gibson went off before the corner that led to the winner was also a bone of contention.
"All we ask is that the officials make the right calls and that wasn't the case today," said Foster. "I thought the referee got lots of decisions wrong and two of them were absolutely key decisions in the game.
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