Billing at Pusher is currently done on an account level. That means that if you have only one app then essentially your plan level dictates how many connections and messages you are allowed for that one app.
Your plan level, and therefore limits, only apply to the apps that you are the owner of.
Now imagine you have multiple apps. If your plan allows for 100 concurrent connections (and some number of messages) and you have two apps, App1 and App2, then if App1 currently has 100 connections and App2 has no connections, then you are at the edge of your plan's limits. If some new connections are attempted using App2's API keys then they will fail because you will be trying to exceed your account level limits. The same goes for messages - they are aggregated over all of the apps that an account owns.
If you are a collaborator on other apps then your plan level has no effect on the limits applied to those apps (although remember that billing, and therefore limits, are applied on an account level).
If you have a collaborator on your app that has upgraded their plan and you want their limits to be applied to the app then you'll need to go the collaborators tab of the app in question and transfer the app to that account.