If you beat the game 100 times in a row Samus strips naked.
After you beat Mother Brain, if you could escape fast enough, on the left hand side before you reached the top you could see a small room where two people were having sex.
There was a Minus World-esque area that could be accessed only by bombing yourself a ridiculously long distance up a particular wall.
There are actually strange locations that can be reached with either glitches, Game Genie codes, or emulators. These locations are the result of the game interpreting non-level data as levels, or displaying a room with the wrong tileset.
In Prime, there is a hidden message hinting at the future release of Metroid Prime: Hunters for the DS.
There is a message in Research Lab Aether that begins, "Hunter Metroid ds is showing signs of increased instability." However, this was a year and a half before the name "DS" was even announced; during the development of Prime, the system was codenamed "Nitro." Additionally, there are other Metroid types referenced nearby with designations like "dq." It may also be a typo for "Hunter Metroids (are) showing signs..." with the verb changed in a later copy editing step.
There is no easy way to kill a Fission Metroid.
Often repeated in criticism of the game's final room before the Metroid Prime boss. The normal way of killing a Fission Metroid is indeed extremely annoying, but they are easily defeated with a single Power Bomb.
Metroid Prime's story is not regarded as canon.
Partially true; Nintendo were so afraid of fan reactions to Metroid Prime that the EU version of the game was forcibly de-canonised and many references to Samus' backstory erased from it, as were, for some reason, references to the Space Pirates having already entered the Impact Crater and built Metroid Prime's armour. However, when it became clear that fans accepted the new game, Nintendo declared the North American version was correct and Prime was indeed part of the greater Metroid universe.
Similarly, the EU version features some drastic gameplay changes and the North American Player's Choice version even more. This has caused many true statements about speedrunning techniques in particular to be mistaken for lies when in fact they're true in some versions of the game but not others.
Similar to the Prime lie, a reference to a lost Metroid game is on the Space Pirate homeworld.
The message in question reads "Experiment status report update: Metroid project 'Dread' is nearing the final stages of completion." Nintendo has denied the existence of a Metroid: Dread, and this is likely either a meaningless message or a joke from the developers.