The Nellis Air Force Base Public Affairs Department said the "incident" happened about 10:45am on Saturday (local time).
Along with four EA-18G Growlers, the RAAF also sent an AP-3C Orion, an E-7A Wedgetail Airborne Early Warning and Control aircraft to Nevada.
Both crew members from the Growler escaped safely without the use of ejection seats.
Red Flag runs from the 29th January to the 16th February and Australia has sent around 340 Royal Australian Air Force personnel to Nevada to train in the world's most complex air combat environment.