Can the wife do anything if I'm 3 months pregnant and my boyfriend is still married to his wife but they are separated?

First, if they were only married for 6 months, they couldn't possibly have been separated for 'a while' - a few months is probably more like it. As to what the wife can do, I assume you mean from a 'legal' standpoint, if so, likely not much to you unless you have significant assets but I be more concerned about what she may do from a non-legal standpoint. As to your boyfriends inheritance, that's sticky. Inheritance can be separate property that wife can't touch IF boyfriend takes precautions such as not commingling marital money with inheritance or purchasing things with the inheritance during the marriage. The best way to resolve everything, is with a simple separation and property settlement agreement if the wife is willing to sign one.