The reason Classic is disabled in vs mode is because it favors characters like Nero who have moves that travel along the ground but have a very small sprite.
The night time version is also disabled for the same reason AFAIK.
No idea why Ryougi's stage is disabled however.
If that's so then why would the stage come up in random select? If they did it for that reason they should keep it out of random too.
It's probably a bug that it's in random.
I assume the cause of the bug is that they disabled them in vs mode but not in training mode, and since they're in random in training mode they're in random for vs mode because fbread never bothered to make a second "random" that only pulls from vs-mode-selectable stages.
It's even entirely possible that random is actually just set to randomly pull from every stage in the game altogether, that being why even stages unselectable in training like Ryougi's can come up.