In many areas, it is possible for a "natural object" (e.g. a Berry tree, tall grass, a large rock, an iceberg, snow or sand piles, etc.) to appear behind an opponent in a wild or Trainer battle. These objects can be hit by certain moves that can target multiple Pokémon like Surf or Earthquake. If the object is hit, it will break or drop Berries and remain in that state until the end of the battle, when the player will pick up an item ranging from Berries to stones and other items.

In the Battle Mansion, the player can fight against a Beauty trainer. After beating her in the English version, her response is "Yes, a mere half year ago I was a Black Belt! Quite the transformation, wouldn't you say?". In the Japanese version, her response is translated as "I was a Karate King a half year ago: the power of medical science is awesome wouldn't you say?!".

Whilst differently portrayed, both versions hint that the Beauty trainer is transgender (black belt is a male-specific trainer class; same for Karate King in Japanese).

The names of Helioptile and Heliolisk seem to stem from Greek mythology. 'Helios' is an ancient Greek titan who is the personification of the sun. Helioptile's Pokemon X's Pokedex entry states that it basks in the sun to get energy, strengthening this connection.

In Anistar City, there is an old man who is depressed because of the death of his wife. He will ask the player to lend him any Pokemon level 5 or under to keep him company. After defeating the Elite Four, the player can return to the house to find that the old man has passed away, and left the Pokemon behind in a Poké Ball with a letter thanking the player, as well as leaving him a Comet Shard. The letter said how the Pokemon you lent him kept him "smiling until the very end."

X & Y is the first Pokémon generation to add less than 100 new Pokémon (not including Mega Evolutions).

The reason for the special Torchic Mystery Gift at launch was likely due to the fact that Junichi Masuda's favorite Pokemon is Torchic.

According to a tourist in one of the hotels in the game, the sixth gym leader, Valerie, is originally from Johto. Given how Valerie also wears a kimono and that her strongest Pokémon is Sylveon, a Pokémon which evolves from Eevee, it's possible that she is related to the Kimono Girls from Pokémon Gold, Silver, Crystal, HeartGold and SoulSilver versions. The Kimono Girls are a group from Ecruteak City in the Johto region who each specialise in Pokémon evolving from Eevee and are always seen wearing kimonos.

Latios and Latias were found to have Mega Evolutions before these forms were officially revealed by Nintendo.

There are several pieces of dialogue in the game that reference the 3rd Generation games, Ruby and Sapphire. It's thought these pieces of dialogue were references to the 3DS Remakes: Omega Ruby and Alpha Sapphire.

Some time after X and Y's release - and even after the release of the game's official soundtrack - a re-mastered version of the World Champions theme from Pokémon Black and White was discovered in the game's data and decrypted by the Pokémon community.

Within the game's files exists three unused sound effects which are all copies of the Pokémon Center's healing machine sound effect. It's thought they were used for testing player-related sound effects during development.

When battling Mewtwo, Articuno, Moltres, or Zapdos in the wild, a remix of the wild battle theme from Pokemon Red & Blue will play. The remix includes 8-bit portions of the song, seemingly taken directly from Red and Blue.

In celebration of X & Y, a short lived Pokémon Center was opened up in Paris, where Kalos was based off. An exclusive Poké Ball-patterned Vivillon was distributed at the store.

The name "Viola" (the same name as the Santalune City Gym leader) is not allowed as a player or Pokémon's name. This is likely because "viol" translates into "rape" in French.

The boy band "Union J" changed their names to "Union XY" for one day to celebrate the release of Pokémon X & Y.

There is a Pokémon Ranger that will ask the player to join Pokémon Ranger team, saying that they could be the Blue Ranger. This is thought to refer to the Power Rangers, an American TV series that takes much of its footage from the Japanese tokusatsu Super Sentai. The characters are superheroes called "Rangers" who fight in color-coded outfits.

An NPC informs the player that Blue, the player's rival in the original Pokémon Red & Blue, has previously visited Kalos to study.

An NPC in the game questions the appearance of a Mega Pokemon, asking, "do you think all Mega Pokemon have spiky hair?" This is a reference to the Super Saiyan transformation in the Dragon Ball series.

When using Surf with Lapras in the game's overworld, the player will be shown riding a Lapras rather than the black creature that appears when Surf is used with any other Pokémon.

Artwork from the "Fossil Excavator" card appears in the art museum of Lumiose city.