I had the same experience!
I have a cruise in 3 weeks, went to check-in, and my paid-in-full was showing a balance due of $0, and things like $365, $750, or $1500, depending on the browser/when I refresh.
I couldn't figure out the math, but some of the balances due matched things I didn't pay for, like FAS+, or unlimited internet. I checked-in without issue and got my eDocs. NCL also confirmed to me in chat that there issues.