best of luck dude, you seem on the level, trust your judgment, you know her better than any of us. just keep your BS radar ticking over, at least until the storm passes, if she cannot see why you were bothered, and explain the relationship with her friend then I believe there is reason to call shenanigans.
in my experience women are too quick to claim you don't understand, and then cry.(I was not a bastard, i just was on the scent of her cheating trail and she used every emotional blackmail trick in the book to control the situation. she was cheating.)
Its really hard to break away from a cheating partner, because you just see the way they look at you, and never notice the way they look or speak to others.
im not trying to freak you out, but in my experience, people who are dishonest, really know how to emotionally pull the wool over your eyes, because they have done it their whole lives.
again, you know your situation, you know how it is, and your alarm bells are ringing for a reason. if your partner of 3 years reacts strangly to your fears, you either have a hole in you communication or a deeper problem.
in my experience, in hindsite, my gut has always done right by me.
communication is the key, but seperate from emotion and observe the behavior. I dont envy you and your position.
trust your gut and heart over any advice anyone gives you.
best of luck mate.
Sometimes I like to use words out of contents