Server creates duplicate player entitys when player login in to the server. I was not login to check it, But when i see the server log thread saying "player (username) loged in with entity id (ID number) at (Cordinates x, y, z) too many times for the same player, i can figure what happened there.
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I just experienced this as well. When I got back on the server, I could kill the duplicate and as a result duplicate my items.