dealing with SO's baby mama

I encouraged my SO to be smart and <a href="">nurture</a> the relationship with his baby mama so he can have more access to his daughter. Now that he's doing that it's stirring up a lot of emotions for me....
His daughter is 9 months old, the mother was his ex, they were together for 3 months, she was supposedly on birth control....then she just disappeared with no explanation. 4 months later she said I'm pregnant and it's yours. She has been very difficult ever since then.
Now my SO and his baby mama are face timing regularly and I think it's a good thing but it also makes me feel...uncomfortable. She's the mother of his child, she has all the power, etc. 
Has anyone been through something like this? Do you have any advice or experiences that you can share? 
Me and my asap have a great relationship and trust each other, I've just never been in a situation like this before.