The (A)GPL has no problems with the app store. It merely requires that users must be able to install altered versions and that’s certainly possible. It’s the app store policies by Apple that forbid GPL apps.
Missing a CLA seems like an oversight, releasing the public code under a license forbidden by Apple’s terms is most likely a deliberate choice to block competing app store submissions. They’d just use LGPLv2.1, Apache License 2, or so.