As I understand it, the two of you are separated and you're worried about this being a sign of her establishing a life of her own.
First, how do you know that there was a credit check done? Did you open mail addressed to her? Are you aware that doing so is of questionable legality?
Yes, if she had that done, she was almost certainly applying for her own account. There are places, as mentioned above, where she can get a phone no matter what her credit is like.
You don't say how long you've been separated, but cell phone accounts are frequently used by one party as a "leash" over the other, via threats of cutting off service, monitoring call activity, etc. It only makes sense for her to want a separate account if this is a serious separation. If you've done anything like I describe, you're acting very unloving and driving her away.