SMZ3 has added keycards to SMZ3 to gate things outside of normal game logic. Below is a list of the keycard door locations. Plan your route accordingly. This information is pulled directly from the source code:
Keysanity Keycard Door Locations

AreaKeycardDoor Location
CrateriaoneLanding Site - Door to gauntlet
CrateriaoneLanding Site - Door to landing site PB
CrateriatwoBefore Moat - Door to moat
CrateriabossBefore Tourian - Door to Tourian
CrateriabossBefore Bomb Torizo - Door to Bomb Torizo
 
BrinstaroneBlue Brinstar - Door to ceiling e-tank room
BrinstartwoGreen Brinstar - Door to etecoon area
BrinstartwoPink Brinstar - Door to wave gate e-tank
BrinstartwoPink Brinstar - Door to spore spawn super
BrinstarbossPink Brinstar - Door to spore spawn
BrinstarbossBefore Kraid - Door to Kraid
 
Wrecked ShiponeOutside Wrecked Ship West - Door to Reserve Tank Check
Wrecked ShiponeOutside Wrecked Ship West - Door to Bowling Alley
Wrecked ShiponeGravity Suit - Door to Bowling Alley
Wrecked ShipbossPre-Phantoon - Door to Phantoon
 
MaridiaoneMt Everest - Door to Pink Maridia
MaridiaoneAquaduct - Door Towards Beach
MaridiatwoPre-Botwoon - Door to Botwoon
MaridiatwoPre-Colloseum - Door to Colloseum
MaridiabossPrecious Room - Door to Draygon
MaridiabossCactus Alley Door changed to a Boss Door (reasons)
 
Upper NorfaironeBusiness Centre - Door Towards Ice
Upper NorfaironePre-Crocomire - Door Towards Ice
Upper NorfairtwoLava Missile Room - Door Towards Bubble Mountain
Upper NorfairtwoAfter frog speedway - Door to Bubble Mountain
Upper NorfairtwoBelow Bubble Mountain - Door to Bubble Mountain
Upper NorfairtwoLower Norfair Escape - Door to Bubble Mountain
Upper NorfairbossPre-Crocomire - Door to Crocomire
 
Lower NorfaironeWorst Room In The Game (WRITG) - Door to Amphitheatre
Lower NorfaironeExit - Door to "Reverse Lower Norfair Entry"
Lower NorfairbossPre-Ridley - Door to Ridley