I started to do an investigation into my WW call log and noticed that the most recent call log for her is not recording data. Should I assume she has found a way to bypass this? She found out I was checking the call logs a couple of days ago and the last incoming call it shows on her usage was Sunday... that can't be right because I know I texted her and facetimed her yesterday and I know others have texted her. Any other apps out their that she could possibly use.

We are currently separated, her choice and she is staying with her parents and I can't access the Iphone without her being around.

I bumped a thread called Hidden Apps for you. I don't understand any of this because I do not use a smartphone, but I hope that thread will answer your questions. If I find another I'll bump that too.

Is it possible she is simply using iMessage? Texts sent that way will not show up on the phone bill. I believ Facetime is all data as well, so that won't show up as a call as far as I know. Assuming you have an iPhone as well, texts sent via iMessage will show up with a blue background instead of green.

But shouldn't that show up in on the Call log or billing information?

I think I am going to try and install this app on her phone:
http://www.teensafe.com/

I am not sure when though...

No, it will just show as data and will be lumped in with all other data on the bill including web browsing, app updates, email, etc.

I agree that she is probably using iMessage. I don't think there is a way to bypass call logs. Only voice calls and SMS text messages will show up on the call logs.
iMessage and Facetime don't show up as texts or calls because they use WiFi or Data to make the connection.

I don't have experience with spyware or if it can track iMessage or Facetime.

I don't know personally, but isn't there a way to shut iMessage off? I remember ages ago when I first got an iPhone, it asked me if I wanted to use iMessage, so there must be a way to shut it off? Can you test it on your phone and then shut it off on her phone when you can get your hands on it?

Yes, iMessage can be turned off in Settings. His WW would know though because her message bubbles would be green instead of blue.

Good point!