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.
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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.