The may or may not be a big deal... More importantly... Does the B have enough clearance at the first fret to play as an open string? If you need to keep the string, and it moves around in the nut, you can take little pieces of paper to shim the string into place so it is more secure in the nut... This will also shim it higher to clear the 1st fret if needed.
If you bought it from a reputable online retailer or in a store, and they said it will work on your instrument (or said it was a specific scale length and sent you a wrong part), they should make it right for you. (at least thats what I would do )
Since the string has already been strung through the body, you may or may not have a notch where the string went over the saddle... Keep an eye out for that.
Had this problem once. I just stuck a piece of paper under there to keep from fretting out the open string. If you're not buzzing though, I see no need to fix what ain't broke.
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