Missed call notifications from voicemail are different to missed calls on your phone.
If a call rings on your phone, and a VM is left, you get notification of that. If a call rings on your phone and no VM is left, no further notification is sent.
If a call doesn't ring on your phone, then VM will either send a notification of message left, or of missed call - depending whether a voicemail is left.
If you don't want to receive notifications of calls that went straight to VM and didn't leave a message, you can use the voicemail menu options to disable these. From memory it's one of the choices on option 3 "settings & features"
