BungeeCord comes with a module system that allows certain BungeeCord functionality to be split from the main code base. Each module handles the command in it's name. For example, "cmd_alert.jar" handles the /alert command. For details on what each command does, see this article. Some plugins will override the commands included by default in BungeeCord, in order for these plugins to correctly function the module corresponding to the overwritten command may need to be removed so that the command is opened up for the plugin to claim.
You need to edit the modules.yml file to remove a module.