Is it the fuel pump keeping prime or is the fans kicking on? I thought it was the fans - never really listened carefully, but on mine it always happens after the fans are finished.
Mine will do that for a few minutes after a ride. Coworker's coming up to me after a lunch ride: "you know you're bike's beeping, right?" Usually once every minute or two up to ten minutes after shutoff, and as others have stated it's to keep the fuel lines primed... you'll hear a little beep, then a short little whir of the pump, then silence again. Completely normal!