The Asian Football Confederation (AFC) conducted a limited re-draw at their headquarters in Kuala Lumpur to include the two sides alongside 24 others taking part in football at the Games, which begin next month.
Agence France Presse quoted AFC secretary-general Windsor John as saying that games organizers failed to pass the names of UAE and Palestine to his body for the initial draw, even though both teams had attempted to register.
John said he was not sure what caused the problem, adding "it could be some computer glitch, it could be some communication breakdown".
He stressed the AFC was not running the competition, and was conducting the draw on behalf of the Olympic Council of Asia and the Indonesian organizing committee.
Eris Herryanto, secretary-general of the Indonesian committee, told AFP the two sides had not properly followed the registration procedures.
"They did something wrong. For example, if they registered one person more than they should have had, that won’t go into the system," he said.
Palestine was placed in Group A with Indonesia, Hong Kong, Laos and Taiwan. The UAE was placed in Group E with South Korea, Kyrgyzstan, Malaysia and Bahrain.
The Games are being held in Palembang and the capital Jakarta from August 18-September 2.
