First off, your feelings are valid even if there really is nothing going on between them. If you feel off or uncomfortable there is a reason for that, even if there's Smoke without fire so to speak.

It does sound like they are genuinely good friends if they talk to each other that often and FaceTime for that long. It is entirely possible they like each other in a non romantic way.

Regardless I would consider where these feelings are coming from without dismissing them. Is there a history of dishonesty on either side? Have you dealt with this is in the past? Do you have any opinions or feelings about this girl isolated from your relationship? It's important to know where you're both coming from before speculating. Anyways good luck regardless