This prototype has a few glitches in it.
If you use a ninjitsu technique just as a stage starts, the colors of the background will be messed up. This can cause different effects, such as enemies not being visible, and even the background not appearing at all. If you use your ninjitsu too early the prototype will freeze up.
If you die during the elevator platform stage of the second round, wait around when you respawn. The elevator will eventually move off without you! In the final this was changed so Joe always respawns on the elevator platform itself.
Go into either of the secret areas of the cave stage in round one. Once there, move in front of the boxes you can see, then jump and hold up to grab onto the ceiling. Now throw a shuriken. Now hold down and press jump and Joe will let go and fall through the floor. You can usually get him back out, but it is also possible to get him stuck in the wall. For the final version, this was fixed, and the secret areas were changed.
Doc Lithius noticed this one. If you select 0-30 shurikens in the options menu and then start the game, your shuriken counter will go to zero if you collect any shuriken items in the first stage. Once it is at zero, it will stay that way, no matter if you try collecting more shurikens. This was thankfully fixed for the final version.