If Samus speeds through a Morph Ball puzzle or boosts through a Morph Ball tunnel, sometimes there's a little door blocking the way. According to programmer Zoid Kirsch, these doors were designed to resemble and serve the same purpose as the regular big doors that open once the force field over them is shot and the room behind them is fully loaded.

When they first started making the 2D-styled Morph Ball areas, they were connected to various rooms with tunnels. They worked well until testers started beating the load times of the next room and would fall out of the world. Kirsch had to go throughout the game and add the Morph Ball doors into every tunnel that crossed rooms to ensure that Samus won't roll out of the tunnel and fall into the void before the room is loaded. Because the testers were already conditioned to wait at the big doors after the force field was shot, no players ended up backtracking and waited for the small doors to open, rendering them a successful change. Ideally, players shouldn't see the small doors very often as the load system tries to get the next room loaded, but they might bump into them if they are quick enough.