Subsequent inspection of the bike on its return to the bivouac identified the problem as contaminated fuel, with a significant amount of water found to be present in both the fuel tank and the fuel pump on Short's bike.
Water was also found in the fuel of Short's Monster Energy Yamaha teammate Franco Caimi when his fuel tank was drained after the stage. Fortunately for the Argentinian, the fuel contamination wasn't as severe as that of his teammate and he was able to complete the day's stage.
As the contaminated fuel that caused the problem for Short was supplied by the organisers, and was therefore outside of the team's control, the Monster Energy Yamaha Rally Team lodged an official request to the FIM to freeze the results of the stage at Checkpoint 2. This would have allowed Short to start the race today. This request was rejected and, as a result, Short will play no further part in the 2021 Dakar Rally.
Because of the fuel contamination, the fuel tanks on all four of the remaining Monster Energy Yamaha Rally Team bikes had to be drained and the fuel pumps replaced ahead of today's 629km Stage 3 around Wadi Ad-Dawasir.