Re: feeling neglected.
"i told her sense she lied about it, then she could no longer be friends with him."
Can I be totally honest with you here? That's the kind of thing my father would say to me when I was 15. To hear that from my husband would probably be about the biggest turn off ever. Not to mention it would irritate the hell out of me that he thinks he can just dictate my life to me like that.
Now, with that said, I'm not saying she should still be friends with him like this. She did lie to you about their friendship, which does make it suspicious. The question is, have you ever had a reason not to trust her before? If you haven't, then it's possible this is nothing more than you got jealous over something that wasn't a big deal. I'd just tell her you're sorry but that this, this, and this made it look like she was up to something. Ask her to stop hiding things, and to not be friends with him anymore, or at least not to see him alone.
If you strongly feel that she was having some kind of affair and you really want her to not be friends with him anymore, I'd find a way to phrase it that doesn't sound like a father punishing his child. As I said in the beginning, that would be a huge turn off to me, and even if I weren't doing anything wrong, I certainly wouldn't be in the mood to have sex after that.