Do you have (ahem) a common surname? And maybe you are very good looking?

FLY will show the booking agent all the passengers that are currently not yet boarded. Usually agents just look at one box with the numbers boarded / not yet boarded, unitl the last stages when they start to look at the stragglers. The passenger name level gives some useful data such as whether the missing passenger has lounge access or is coming in from a connecting flight. So my theory is the agent saw your name - or thought they saw your name - realised you were on the bus and thought "that person I remember but maybe they didn't do the boarding pass correctly". Hence you were called back to the scan point, at which stage you proved that you were correctly boarded. Now there are several possible explanations but it may be there was someone else with your surname and the agent got you confused and/or in between times your Doppelgänger had been cleared down by another agent (for example).

It's just speculation on my part but the agent knew your name - so that was on FLY - and FLY also had you boarded. So similar names and a temporary mix up may explain this. Or it may have been something else.....