glitch Pokemon are mainly from Pokemon red/blue/yellow. There were these glitches in the game which make these 'glitch Pokemon' which look like a bunch of random pixels. The most common and popoular glitch Pokemon is missingo, which can give you unlimited masterballs and looks completely different depending on what name your character has. There is a bunch of glitch Pokemon that has mass effects on the game, such as the super glitch and much more.
for all glitches and glitch Pokemon: http://bulbapedia.bulbagarden.net/wiki/Glitch_Pok%C3%A9mon