Super Metroid could be made unwinnable this way: With a little bit of Sequence Breaking it is possible to acquire the Gravity Suit early, and ultimately reach Tourian without ever collecting the Varia suit. The catch is that each Suit cuts damage by half (both suits = 1/4 damage) ... but this is a moot point if the player is especially adept at avoiding damage. Most Energy Tank upgrades are optional, and Tourian's final Save Point is located beyond the Point of No Return. The problem? Without the Varia Suitnote And, for some reason, this one check only looks for the Varia Suit, Mother Brain's unavoidable Hyper Beam attack inflicts a whopping 600 points damage, and if you don't have enough E-tanks to survive one Hyper Beam, the final plot event (where the baby Metroid rushes in to save Samus) never triggers...since you died before it could take place.
A player who is very adept at maneuvering Samus before she gets her mobility upgrades (like the Gravity Suit) can find themselves stuck in certain spots with no way out. While the game tries very hard to prevent this with the appropriate obstacles, it is very possible to enter later rooms of the aquatic area Maridia with enough bomb-jumping and wall-jumping. A player needs to be careful when doing this, since there is a room or two with quicksand. The sand usually just pulls Samus down to the bottom of the pit the longer she goes without jumping- all the player needs to do is jump up the sand. However, being underwater reduces Samus' mobility (without the above Gravity Suit). Being in quicksand further reduces her mobility. As long as she has the Gravity Suit (which should have been obtained by that point), she can nullify the underwater movement restriction and get out of the sand with a little bit of jumping. But without the suit, she suffers twice the movement penalty, sinking down faster than she can jump up, effectively making it impossible for Samus to ever escape this watery grave. Without the Hi-Jump Boots, there is no way out.
Metroid Prime 2 includes a number of rooms that have several switches that must be shot in order to progress. If the player triggers some of the switches and then leaves the room, the game becomes unwinnable (or some items become inaccessible, depending on which room) because the game resets the counter but does not reactivate the switches.
You can also trigger a super-jump glitch while fighting the boss Chykka, letting you leave the room (the doors don't lock). If you do this, however, then Chykka is gone for good — along with the reward for that fight, the Dark Visor, which is required to beat the game. You can play with the super-jump glitch safely, but only if you beat Chykka first.
The first Metroid Prime game had a similar Unwinnable bug that was fixed in later releases. When you beat the Phazon Elite, the doors unlock and he leaves behind the Artifact of Warrior. If you're careless enough to leave the room without collecting the artifact, then it will never return.
The Wii "Trilogy" re-release uses the original Metroid Prime version as a base. Even though some elements from later versions (such as Fission Metroids in Omega Pirate's room) were added in, it retains this bug. Oops.
Metroid Prime 3 has sequence breaks that allow you to get the Spider Ball earlier than you're supposed to. However, if you then use this to get the Hazard Shield before beating Gandrayda, you're stuck - the Hazard Shield is replaced by a missile expansion which you can't pick up, and as such the enemies that are supposed to break open a window for you to escape afterwards never spawn.
In Metroid: Other M, there's a glitch that can occur late in the game once you can use the Beam Grapple and are ordered to hunt down Ridley. There's a certain door that Adam unlocks by this point that you access by using the Beam Grapple. However, should a certain thing be done, this door would be locked and would not open no matter what you do. Now there are two possibilities for this glitch: The one theorized by fans which states taking down the Rhedogian and then going back to a previous Navigation Room and saving there, and the one stated by Word of God that claims the cause is picking up the Ice Beam, going into the next room and killing the enemies there to open the next room, then going back to the Ice Beam room before progressing to the room you unlocked. Regardless of which one it is, the only thing to do at this point is start over. To avoid this, do not backtrack to the Ice Beam room until you enter the second room after it at least once, and do not backtrack once you encounter the Rhedogian (the first and third battles, to be specific).
Not even the original Metroid is safe. If you are careless, you can bomb through the bridge to Tourian, and the lava/acid under neath makes it impossible to jump back up before whatever block you destroyed respawns.
In Metroid: Zero Mission, it is possible to be forced to reset and start from your last save right near the end of the game on Hard mode. In the second half of the game (The Mothership/Chozodia), save stations also do the dual service of refilling your health and ammo. On Hard mode, a couple of those save stations are simply walled off and inaccessible. Once you get your suit back and are going back through the game item-hunting, be very careful when you loop back around to the Chozo Ruins, because once you get your suit back, several obstacles will be placed throughout the ruins that require power bombs to destroy. On your way to get one of the power bomb expansions, you'll fall through a collapsible floor with no way back: the only way out is forward. On Normal mode, there would be a save station right after with a chance to refill, but on Hard mode that's one of the stations that's walled off. In order to progress forward and get out of this area, it is absolutely mandatory that you have at least two power bombs in tow. If you don't, well...
In addition, what makes this somewhat frustrating is that power bombs are scarce at best on Hard mode, so it's easy to run into this while doing a final item-sweep and not realize it until it's too late. You'll either have to get lucky with the pickups or go out your way to a Chozo statue or Mothership/Chozodia save station to refill. And the Space Pirates (the only enemies you encounter in this section) drop next to zero pickups whatsoever.