Short version: A distracted Chauncey didn't supply Perry with enough quality men. Perry submitted a transfer request which wasn't acted upon until after his (Perry's) victory on Lake Erie. Perry's bold moves carried the day; all forgiven.
Read a more detailed description taken from The Fight For A Free Sea: A Chronicle of the War of 1812 below (for even more detail, go to the link):
The quick temper of Perry flared at this. ...and he had rightly looked to Chauncey to supply the deficiency. Impulsively he asked to be relieved of his command and gave expression to his sense of grievance in a letter to the Secretary of the Navy in which he said, among other things: "I cannot serve under an officer who has been so totally regardless of my feelings. . . .
Most fortunately Perry's request for transfer could not be granted until after the battle of Lake Erie had been fought and won.
Perry's indignation seems excusable. Perry had not enough sailors to defend his ships, and the regiment of Pennsylvania militia stationed at Erie to guard the naval base refused to do duty on shipboard after dark. "I told the boys to go, Captain Perry," explained their worthless colonel, "but the boys won't go."
On Lake Ontario, Chauncey dragged his naval campaign through two seasons and then left the enemy in control. Perry, by opening the way for Harrison, re-won the Northwest for the United States because he sagaciously upheld the doctrine of Napoleon that "war cannot be waged without running risks." Behind his daring, however, lay tireless, painstaking preparation and a thorough knowledge of his trade.