My HTC One M9 runs fully updated Android 5.1. When I first turn on the mobile and make sure it's not silent nor on vibrate and the ringing volume is at max and I receive a phone call, it rings as it should. Then when I receive a message on whatsapp and the phone makes the message tone normally, after that when I receive phone calls the phone only vibrates. There is no ring tone, it's still on max volume and messages make their ring tone normally and even the alarm is fine, it's just the incoming calls that are silent and only vibrate.
I tested the idea that whatsapp is doing this by rebooting and testing an incoming call before and after receiving a whatsapp message. It happens every single time.