I absolutely agree to what @jhuan said. Since you have the SuperSurf - Viber, Skype, WeChat etc are free. These applications are dependent on your phone's data connectivity.
If you already have your bill. Try to go over the line item (the charge for the phone call). Then compare it to your phone's call history/register.
Enjoy the rest of your Thursday!
i dont use skype but one thing im sure with viber is that, if you dont have internet connection, there will be an option to call via the normal flat rates. its possible that u made a call without noticing this option is enabled therefore it will reflect as a regular phone call. try disabling that option in viber.