In the original version of Metroid Prime 3, Admiral Dane shouts, "Damn! They're targeting the planetary-defense system." The word "Damn" was replaced with "No" in the Metroid Prime Trilogy though, likely to remove a possible swear word from the game.

In Metroid Prime, the wait time for doors between different rooms to open can sometimes last a long time, because it acts as a buffer to allow the room past the door to load in. In most cases, two rooms can be loaded in at once, the one Samus is in, and the one she is going to (on rare occasions three rooms can be loaded in), and in rooms with multiple exits, only one door can be open at a time.

According to programmer Zoid Kirsch, the game's developers went with the design of the blue force field on the doors that fades when shot to indicate the door is "ready" to open, but has to wait until the room behind it is loaded. Most times, the room should already be loaded by the time Samus gets to the door, but some gameplay elements like the Morph Ball make it so she can get there much faster. On the GameCube and Wii disc copies of Metroid Prime, this means you will have to wait for the disc to be read and finish loading the room for the door to open, but on a digital copy like the Wii U Nintendo eShop release of Metroid Prime Trilogy, the load times are much faster since the game is stored on the console's internal memory with no other changes to the game.