Late on Monday, it emerged that Yamaha had discovered that water had made its way inside the fuel tank and fuel pump of Short's bike after the American rider ground to a halt shortly after the second refuelling stop on that day's Bisha to Wadi Ad-Dawasir stage.
Short was unable to get his bike restarted and became the first factory rider to drop out of the race, having concluded the opening day of the rally in 10th overall.
Following the discovery of water in Short's bike, Yamaha contacted event organisers ASO, who subsequently admitted that the fuel supplied to riders had been contaminated, and requested that the final 190km of the stage be retrospectively disregarded.
#6 Monster Energy Yamaha Rally Team: Franco Caimi
Yamaha also confirmed that Franco Caimi, who finished down in 31st on Monday's stage, was affected by the same problem but was able to continue as the contamination was less severe.
Heading into Tuesday's third stage, Ross Branch was Yamaha's highest-placed rider in the overall classification in third, followed by Adrian van Beveren in sixth.