Do I tell him to cut his ex or do I leave?
I got into a relationship with someone for almost 3 months. He is very close with his ex that was with him for 9 years. They constantly are messaging each other. I am uncomfortable when I am around them so I chose to not be around her. What do I do? My mind I wanna stay with him but I can’t be comfortable with her around.
9 years is a lot of history and your guy needs to get over his ex before he can be with you 100%. By your post, he's still attached to her and vice versa to a certain extent, and you either wear it or you don't. If you tell him to cut his ex, he won't and possibly can't as of yet, because she's still 'there' in his heart.
3 months is pretty much early days and you're still finding out what and who makes your guy tick. If he can't respect you and your relationship together, then you need to be kind to yourself, and look at it from a distance and determine what is it about him that makes you happy and unhappy, and weigh up is he worth being with at present when his emotions are 'all at sea'.