There is Japanese text in the out of bounds regions of certain levels. Its purpose is unknown.
Area N in particular contains otherwise unused tiles in these regions.
Only some of these texts can be easily translated. Most of them are a combination of "上" - up, above and "共" - same, together. All of these end with a number followed by 上.
There are unused colored sprites of Model O in the game.
The game itself uses a browned-out variation of one of the sprites, and the semi-Biometal itself is named "Mysterious Stone".
Though Model O is not obtainable in easy mode, using cheats to obtain it will use these sprites when Vent or Aile are saved from bottomless pits by the Biometal. This implies that Model O may have been intended to be obtained by defeating Omega in easy mode.
Omega has some leftover frames of animation that were originally used in the final scene of Mega Man Zero 3 after he had been defeated. These can't be seen in-game without modifying the ROM.
The game contains several card keys, each with a color, but one of them, "White Card Key", is unused. Its description is "It doesn't take a genius to figure out this opens white doors." There are no doors that require its use.
The game contains a debug room with several features for testing, which include normal surfaces, walls that can't be climbed, a slippery floor, a moving floor, a sinking area, one ladder, water, and spikes. The room can be accessed with the Action Replay code, 22160484 00000000.
Aside from the logo change, the "Rock On!!" text found on the left and right of the bottom screen is also removed in non-Japanese versions of the game.