A few things jump out from the logs (where I only see reference to 3 containers):
• were there multiple agents at one point? It looks like some of the code locations previously (or even currently) belonged to another agent and weren’t properly cleaned up
• when a location is updated, the agent performs a blue/green deployment where it first stands up a new container and then shuts down the old one. Did you recently reload a location? It’s possible both the new and old containers are still up while it’s transitioning.
• does the agent service any branch deployments?