I doubt they're using floppy discs for this. At least I hope they're not. Where would you find a computer with a floppy drive nowadays anyhow?
Oddly enough, there is an interesting constant in all of these errors. The erroneous transfer listings are either from different lines or from reroutes on the chosen line. The 14 St-6 Av transfers come from the line, the Union Tpke transfers come from the to 179 St option Meanwhile, as N6 Limited stated, the transfers shown on the option come from either the or lines. There is also the numerous reports of the "(N) to Manhattan" appearing at Coney Island on the options. That obviously comes from the via West End option.
Like I said, hopefully this is fixed sooner rather than later because frankly, this is just ridiculous.