According to the game’s Japanese publisher Square Enix, the swastikas appearing on flags in the game’s “zombie mode” were changed to the Iron Cross in the dubbed console and subtitled Windows versions. This change, however, was not made for the subtitled home console versions.
The reason for the change in the dubbed home console versions could be related to the fact that a counterclockwise swastika, or manji as it’s called in Japanese, is traditionally used in The Land of the Rising Sun on maps to denote Buddhist temples. This mark, of course, has no relationship to the Nazi party. See the comparison above.
Perhaps, because the game is dubbed into Japanese, the inclusion of swastikas with Japanese voices might cause confusion for some players. That, however, doesn’t explain why the symbols were removed from the Windows version. Kotaku is following up with Square Enix and will update should the company comment.