I’m proposing a PR (hopefully) fixing the problem : https://github.com/sailfishos/sailjail-permissions/pull/124
It is coming from the fact that the phone application is prestarted and prestarted application rights are not declared exactly the same way than normal applications. As far as I understand, the phone application run inside sailjail, without prestart, should work, because it is declared that it can own “com.nokia.telephony.callhistory” DBus service. But the prestart version doesn’t have this ownership granted. This service is used by the notification system to set the action on a miss-call.
I’m not sure the PR I’m proposing is the right way to do it, but let’s see what the reviewers will say.