Hmm....it *might.* I don't own that particular pair of jeans, so I can't say for sure. Both my pairs of J. Crew clamdiggers have the ink problem, and I've soaked them in vinegar and washed them on hot, etc. and nothing has worked. The ink continues to come off. I'm going to try some commercial dye fixative and see if that works. At first it didn't really bother me, but now it's actually kind of annoying. I couldn't find any other clamdiggers that worked for me though.
Maybe someone else who owns your Muse jeans can say whether the problem will go away with repeated washings or not. My inclination is to tell you to take them back, though. I'm constantly washing or rubbing blue ink off all my clothing/handbags/hands. It's just not worth it. I'll be looking to replace my clamdiggers next summer for sure.