Known bugs

Known bugs in Pokémon Fusion Generation
 * The game may crash during certain rival battles.
 * Avoid this error by: saving your game
 * before you enter Pokemon Tower in Lavender Town for the first time
 * before you leave Oak's Lab after getting the Master Ball
 * before departing Viridian City for the Indigo League
 * Cinnabar Island and parts of Seafoam Islands are laggy.
 * Cinnabar Island fly icon is not visible (but you can fly there).
 * Transform can cause crashing if used by the player's Pokémon.
 * Avoid this bug by: refraining from use of the move Metronome.
 * When you run out of Safari Balls sometimes you are not transported out of the Safari Zone and can continue to throw safari balls even though you don't have any.
 * Illusion ability effect is permanent, doesn't break like it should.
 * Some sprites are distorted in certain copies of v1.2 (the version with Time Capsule enabled).
 * This is easily corrected by getting a new copy.
 * In older versions of the game approaching Bill while he's getting attacked by Beedrill may crash the game.
 * Avoid this bug by: saving your game as soon as Bill cries for help and if you think your copy of the game may be outdated get an up to date copy.

Known bugs in Fusion Generation II
 * You may be allowed to use Cold Feet before getting the Legend Badge, allowing for sequence breaking that will negatively impact gameplay
 * Avoid this bug by: double-checking your trainer card to see that you have received five badges before using Cold Feet outside of battle.
 * Player can surface anywhere when diving potentially getting them stuck in a void.
 * Avoid this bug by: only triggering Dive with action button, never from the party menu.
 * The separation process can be used to duplicate items (no known negative effects).
 * Gardenia will sometimes walk through a wall after you meet her.
 * Picking certain berries may crash the game.
 * Avoid this bug by: saving your game before you pick any berries.
 * When surfing on Unova Route 11 the player will not stop surfing when touching the footbridge, only after reaching land.
 * For some players the boss of Laboratory A may refuse to attack.
 * For some players your partner in the very first battle may refuse to use damaging moves.
 * If you stock up on potions and antidotes as soon as you get to Cherrygrove City the battle should still be winnable.
 * The final boss almost always opts for less than optimal moves making the battle too easy.
 * Arbok fusions (e.g., Arbokachu) can learn flying type moves for some reason.
 * Very rarely a runtime error will occur when loading the title screen animation.
 * Opponents' intersex Fusions display as male.
 * Game may crash when selecting Poke Gear options other than phone.
 * Team levels may not reset properly and remain Lv50 after participating in the Conference of Champions.
 * "Script is hanging" when starting the game.
 * Closing as many other programs as you can before and/or disconnecting from the Internet before starting should prevent this error.
 * East Sea Shellos/Gastrodon changes to West Sea Forme when separated from a fusion.
 * It's possible to ride some Canalave City conveyor belts in the wrong direction and get stuck.
 * Using Escape Ropes or Dig outside of battle may cause crashing.

See also: Pokémon Essentials Known bugs