All characters using mismatched ID/Ship/Weapon combinations must possess either an Admin granted Terrorist ID or a Special Operative ID.
Quote:6.10 Player reputation and conduct must match player actions. For instance a player may not dock on a base belonging to the persons whom they are attacking or being attacked by.
Some of your guns have been removed because you're not allowed them with your ID and ship. You have been made hostile to the Rogues because you were told to not dock by a rogue.