From The Rockman Corner:
A little background on this for those just catching up: the build date for this prototype is August 23rd, 1995 - that's about four months before the game hit retail. The differences here are mostly graphical, i.e early stage backgrounds and early sprites (Byte/Mandareera, for example). The unused gate in Blast Hornet's stage (previously seen on the back of X3's NTSC box) is fully operationally, too. Of course, these are just a few of many surface-level differences. Who knows what unused wonders hide inside the code?