@Smin11,
This sounds a lot like what I'm going through myself right now. My BF went out one night and didn't come home until 8am. He said he went to the casino with some of his friends, but then the next couple of days he was messaging some girl on FB. I saw some of the conversation, but then the next day it had been erased.
My biggest problem is that he accuses me of cheating all the time and I am nothing but faithful, yet he still goes through my phone all the time, which I don't have a problem with because I've got nothing to hide. But for some reason he has a problem with me going though his phone!!
If she has been trying to hide this guys information, there is something wrong!! I wouldn't buy into it, you may have messaged this guy and he said he would stop, but that doesn't mean that hes going to stop. I'd keep an eye open, but the best thing to do is go with your gut instinct because its never wrong... Only you can answer your own questions. I don't think you are crazy and I wouldn't even listen to these other people questioning why you are going through her phone. A couple should be able to share every aspect of their lives with each other including personal things like who they talk to. Just don't be that guy that sneaks on her phone in the middle of the night while shes sleeping or in the shower. Be honest and open with her and ask her randomly to see it. If she hesitates or says no, that's a big red flag