The Atlanta Journal-Constitution's Doug Roberson first reported the reason for the six-man bench, which was then confirmed to MLSsoccer.com by a team spokesperson.
Carleton has only made three MLS appearances this season and was unlikely to start. But he has regularly been in manager Frank de Boer's 18-man squad.
Unusually, Atlanta had opted not to travel with 19 players in case of an injury or other unexpected absence, Robertson reported.
Carleton is not the first MLS player to pull a passport snafu this season. The Montreal Impact's Harry Novillo was also kept out of action following a similar incident back in March.