Collaborators don't incur app usage: app usage is only counted and billed against the app owner. This means that to increase the limits of an app you need to ensure the app owner account is upgraded.
If you have accidentally upgraded the collaborator account you have two options here to resolve this issue:
1) Transfer all of the apps to the upgraded account. This can be done by following the instructions at How do I transfer app ownership from one Channels account to another?
2) The second option is to upgrade the owner account and downgrade the accidentally upgraded account.