"com.android.phone has stopped" after dirty flashing CM13
This was because of a change in the code.

As Firelord has said, clear the data for the apps, This can be done like so (this will also delete your SMS/MMS database, so make sure to backup them beforehand):

adb shell
rm -fr /data/data/com.android.providers.telephony/
rm -fr /data/data/com.android.phone/
exit


The -f flag is for force and -r flag means recursive.