I have the latest scale Legacy version, 6-11414, # 612.
Is that what you are talking about? My loco was perfect out of the box, with everything working and paint and graphics as I expected. I would have noticed if the strip was mis-aligned. The only thing I didn't like about mine was that it was not Union Pacific, as i thought it would look better in gray and armour yellow, but a little paint and work to align the stripe there, too, fixed that.
I have the most recent Legacy version.
I have seen four other Legacy N& Js and I would recall if I saw one serious mis-aligned, but I don't recall any. Do you have a picture of one of the mis-aligned ones?