If,as you say,the gf is living at her mother's now...where do you expect them to spend quiet time together? If male friend has his own room,then its natural that his gf will be a frequent visitor. If he was *just* a flatmate you probably would not feel so uncomfortable. I wonder also if your feelings for him are more than just a best mate? You need to put yourself in their shoes. If you had a bf who did not have his own place,wouldn't he spend a lot of time with you at yours?
You either need to accept the situation,or one of you needs to move on.