Munchlax and Bonsly, Generation IV Pokémon, make an appearance in Pokémon XD, despite it being a Generation III game.

Miror B.'s design is styled after Michael Jackson. This is strengthened by them both having a signature glove. Miror B. can also be seen Moonwalking on occasion, and he has a more disco-styled tone to show off his new design.

A Trainer at the ONBS Station has lost their Bonsly. It appears at the S.S. Libra but runs away on being approached. Returning Bonsly to its Trainer gains the reward of the Bonsly Bingo Sheet. This begins with a Bonsly with Rock Slide and allowed players to have a taste of battling with it long before the release of Diamond and Pearl.

In Pokémon XD: Gale of Darkness, if you use Weather Ball under the effects of Shadow Sky, it becomes a ??? Type move.

Most of Dr. Kaminko's inventions resemble the art of Chindōgu, which are inventions that seem to be the ideal solution to a particular problem, but end up being either useless or causing even more problems.

Pokemon XD is one of the few games in the main Pokemon franchise to be a sequel, taking place directly after the events of Pokemon Colosseum. However, before it was released, Reggie Fils-Aime stated in 2005 that this game would not be a sequel to Pokemon Colosseum. Rather, it would be a brand new game. Whether this was something that was planned for Pokemon XD or a case of Reggie being mistaken is unknown.