It is not a restriction of the Canvas itself but an issue with the installer upgrading the web apps. To upgrade all of your web apps to the new version you will need to run installer with a maximum of 10 apps and repeat the process for any extras. Steps:
Leave the first 10 web apps in the Canvas directory, copying the others to another directory.
Run the installer, upgrading the apps.
Remove the current 10 apps and replace with the next 10 that haven’t been upgraded.
Run the installer, upgrading the apps.
Repeat as many times as needed.
Copy all of the web apps back to Canvas and start the service.