For us this happened because the application registration used an identifierUri that has already been used in the past (the app registration was at some point deleted and later created again).
The deleted application registration was still around, in deleted state, so the system didn't complain about duplicate URIs, but something still broke because of it.
In the admin center, it is possible to change the URL of the new application (has to be done through editing the manifest) and restore the original, or delete the old one permanently, which should resolve the problem.