I don't think we should assume that
Scratch was working on her own prior to the breakout from
Eastern Bay. Remember that the only person in We're Alive that we know, beyond a doubt, was in prison on the day of the Zombie outbreak was
Latch. While I assumed that
Durai and the other Mallers were prisoners who were released by Scratch I haven't been able to find anything in the story that actually says that.
What if Durai wasn't a prisoner in Eastern Bay, but rather on the outside, and the mastermind behind a prison break that just happened to come at the same time as the outbreak. Scratch was then his Lieutenant from the outset, along with some extended crew of henchmen and minions. That gives them the manpower to raid
Locked and Loaded before the outbreak, and eliminates any problems with timelines or continuity.