When you complete the frequency section (2nd section), a cube planet flies across the screen, yet it seems that it is random. The time the planet flies across the screen differs in a range over 20 seconds (sometimes at around 1:35, sometimes 1:50). No idea if this affects any other gameplay.

Sometimes in the third section (cube planet), the robot launcher comes earlier or later, so that it may be impossible to hit the planet immediately as it comes out.

I don't know if the planet that appears after the frequency section has anything to do with the robot launching section, just putting it out there.

Might be a bit farfetched, but some glitches might also occur based on what objects and their positions are in the start, as each time you start the game, the objects at the start screen differ and have different locations.

To also add to this, replaying it several times also have different effects on the items that come out during the ending cutscene, along with other things. Perhaps the timing of events is also effected by this? Stopping halfway and restarting also seems to have an effect as well, but unsure what exactly.