It is not a natural glitch, and it requires a firmware exploit (which are technically available without a cheating device) or otherwise a cheating device.
This glitch is caused by attempting to load the Super Training touch screen menu with a Generation VI 724+ glitch Pokémon, or Generation VI glitch Egg glitch Pokémon.
This causes the game to no longer load any map connections, causing what appears to be a void similar to those seen in the Tweaking, broken escalator glitch and Elite Four door glitches from Generation IV. Attempting to use an item with Y may also freeze the game.
This 'half-frozen' effect is reminiscent of the Nintendo DS Sleep Mode exploit, in which generally the game will freeze when the player attempts to do certain actions.
The 'void' cannot be explored and is more of an invisible wall. This classifies it more of a web.