Seriously if some people don't want to tell you anything they won't. Men/Women can be caught red handed in bed with someone and they still won't admit anything has happened!
WHY do you think she isn't telling you the truth? I know you probably swing between believing her and not, but what is it that niggles away at you? That something doesn't add up? Your instinct? Or paranoia?
You really have two options: accept what she's saying as the truth and let it go or you will end up driving a wedge in the relationship anyway. If she's sworn that nothing has happened, there's not much you can do at this point but believe her (if you want to).
If you can't do that, you'll have to just walk away. Which I know you don't want to. Sit down and tell her it's hard for you to trust her because she was texting and calling this guy who was her ex, and you didn't know anything and felt like a fool. She should've been honest from the beginning and you wouldn't be feeling like this. She needs to accept she's done the wrong thing here and own it, and help you to move forward and trust her.
There are no easy solutions, and every relationship is different so at this stage, it's completely up to you how you feel. If time goes on and nothing happens and you feel you can trust her, the mistrust should start to fade. It's just right now that's the tough part.
Go with your instinct