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Poké Ball animation glitch
The Poké Ball animation glitch is a natural glitch in Pokémon X and Y. It only occurs in versions 1.0 through to version 1.2 of the games, and was patched in later updates.
This glitch causes the special animations associated with Poké Balls other than a standard Poké Ball to not show upon starting battle. The effects will show however after switching out the current Pokémon, or attempting to capture a wild Pokémon but the wild Pokémon escaping.
Affected Poké Balls are as such:
The image below demonstrates how certain frames of animations for Poké Balls differs between v1.0/v1.1/v1.2 and v1.3. Thanks Serebii for the image. Original author unknown.
Serebii (image, original person to capture the screenshots unknown)