Speculation: The Mallers or Latch and Sratch at a minimum hit "Lock and Loaded" and broke into the safe.

Speculation: In Mark of the Beast a "weapon" that Latch got from a safe was taken by Scratch. Scratch only want to use it if she has to. This implies limited Ammo. .50cal hand gun rounds are rare. Or, is it something more obscure from another safe. They call it a Weapon not a rifle or shotgun or handgun.

True: Scratch's scar is probably less than a few years old. Latch calls it red. So it was pretty deep and a few years old. Alternatively it could be less deep and more recently.

Speculation: Scratch is called Scratch because of the scar (Duh) This implies that there is probably something to Latch. Latches generally open something. Something that is shut and needs opening is a lock. Opening someone elses' Lock is often an illegal act. Do enough illegal acts and you wind up in Jail. End up in Jail enough and you get to graduate to prison.

Speculation: Latch says it was not very hard, you left the code there... When Latch and Scratch show up at the tower the first time. The "wasn't very hard" implies to me sarcasm.