From the History Channel forum where I initially found out about this incident:
As for the incident with Johnson, he painted the "kill" on his aircraft immediately after the incident was confirmed. To quote Geoffery Pentland, RAAF Colours and Markings 1939-45. Vol 1 (page 70):
"It is a matter of historical fact that the pilot responsible for this act, a well known ace from an even better known US fighter group, later sported an Australian flag in the middle of his victory scoreboard, until its removal was ordered to help in defusing a near-riot situation which had developed between certain Australian and American air units at this time."
At the time RAAF aircraft were "loitering" near Johnson's airfield and death threats against him, and his squadron as a whole, were being made.
Whatever his reason for displaying the Aussie flag on his scoreboard (it may have been a sort of reminder of his mistake, as Mertox suggests), his arrogant refusal to remove it led to a very nasty situation.