- Moving a Rain spawner to the top-right of a section can crash the game.
- Moving Rain to another section does not destroy the Rain graphics in the previous section.
- Brain Break's first form is immune to Flash Bomb.
- The Time Slow clock graphic overlaps the life counter in Wily Challenge, making your lives hard to see.
- Swinging with Thunder Claw when there are spikes behind you can get you stuck.
- Fire Telly does not have a sound effect.
- When Spring Man is magnetized he can pull you laterally through and off ladders.
- Grenade Man's Flash Bomb does not explode on him when reflected by Jewel Satellite.
- Grenade Man's Crazy Destroyer being reflected by Jewel Satellite when about to explode leaves a reflected projectile on the ground.
- Resetting level with Crtl+R (or L+R+A+Start) while boss doors are closing or screen is transitioning will stop bosses from spawning in causing a softlock.
- Crash Man, Spark Man, Pharaoh Man, Crystal Man, Napalm Man, Knight Man and Plant Man can clip in tight spots.
- Star Tile 2 (Alt)'s description contains a typo.
- Mega Ball bounces off Mega Ball Weapon Blocks/Barriers without destroying them, under very specific circumstances.
- If you open a key door, then touch a checkpoint during its closing animation, the key door will respawn after you die or restart, sometimes making the level impossible to complete.
- When activating Flash Stopper, then transitioning to a room with a Rolling Drill, the Rolling Drill has no hitbox.
- Touching a checkpoint after a stage ending boss is killed then dying will result in a softlock as boss will stay defeated.
- Screen transitions and doors will lock up due to 'Malformed Sections' in boss rooms.
- With specific non-standard section layouts, Illusian may not spawn.
- Collecting a key dropped by a boss very rarely crashes the game.
- Jumping through moving platforms from the bottom can very occasionally result in a crash.
- If you press Ctrl+R (or L+R+A+Start) while on a fan for long enough, the sound effect will keep playing.
- If you shoot a regular weapon, then switch to Thunder Claw immediately, your buster stays out until you shoot again or switch weapons.
- Black Hole Bomb can suck up Spring Man's arms when shot.
- Standing close to a Magma Beam, the sparks can still show if the beam has already passed.
- Jewel Satellite dings off of already exploded TNT, despite it not being there anymore.
Version 126.96.36.199 was centered on fixing minor issues and was released on April 20, 2019.
- Moved Concrete BG 3 (Alt)'s waterfall one pixel to the right, to make it align better with the tile grid.
- The tip-toe movement works differently from how it did in previous versions.