In the French version of the game, when challenging Brawly, he says, "ai découvert le secret de la vraie puissance en fixant un Nautile pendant des jours et des jours." This means "I discovered the secret of true power by staring at a Helix [Fossil] for days and days…" This is a reference to Twitch Plays Pokemon: a livestream where viewers were able to play the game via commenting. Due to the chaotic inputs, viewers would often accidentally open up the items menu and attempt to use the Helix Fossil to no effect. Viewers joked about the recurring mistake, saying they were "consulting" the Helix Fossil as if it were a religious oracle.

In Sootopolis City, a little girl named Kiri will give the player two berries every day they talk to her. Her name comes from Junichi Masuda's daughter, Kiri, who was born around the same time as the Japanese release of Ruby and Sapphire.

In an interview with Nintendo Dream magazine, series character designer Ken Sugimori stated that the character Aarune was given a Flygon since it was capable of learning both Secret Power and Fly, which were key to finding Secret Bases.
He also revealed that the reason Mega Flygon was not included in both Pokemon X & Y and Pokemon Omega Ruby & Alpha Sapphire, was because Game Freak had trouble trying to complete a design, so it was dropped.

There is a man in Pacifilog town who says "They say, here in Hoenn, there are places called Mirage spots. One does not simply walk into a Mirage spot. Not to mention that these places also appear and disappear mysteriously." This is a reference to the phrase "One does not simply walk into Mordor", a quote from Boromir in The Lord of the Rings: The Fellowship of the Ring.

Some Legendary Pokemon in the game's data have unused hidden abilities. These include Entei with Flash Fire, Regice with Ice Body, and Amaura and Aurorus with Snow Warning.

Despite being able to be shiny in Pokemon X & Y, Groudon, Kyogre, and Deoxys' shiny forms are unobtainable.

Within the game's files, unused keystones used by NPCs, such as Maxie, Archie, and Steven can be found. They are fully programmed and some even had icons.

If the player successfully brings a Pokemon all the way from Pokemon Ruby, Sapphire, or Emerald into Pokemon Omega Ruby and Alpha Sapphire, then takes that Pokemon to the Game Director in Lilycove Motel, the Director will give them a diploma showing multiple different sprites from Ruby, Sapphire, and Emerald. The player can then hang this up in their secret base as a wall decoration, showing the original sprites of Brendan and May.

A map can be found in one of the houses in Dewford Town that looks incredibly similar to a map featured on Pokémon fansite "Serebii.net", but flipped horizontally. The map is from the site's "Pokéarth" section, which shows the position of many regions from various Pokémon games, such as the Kanto and Sinnoh regions.

The "Hi Skitty Doll" in Sea Mauville is a reference to Hello Kitty.

The couple in Sea Mauville that give you the Destiny Knot are named after the parents in Malcolm in the Middle: Hal and Lois.

The hex maniac found on the first floor in Mount Pyre is a reference to the "Ghost girl" found in Lumiose city of Pokemon X & Y.

In the cutscene where the elite four member Phoebe introduces herself, a mysterious small girl can seen behind the player and her in 2 different scenes. First in Phoebe's chair in the first scene right when it fades, but only for a split second. The second time is in the third scene, with her hiding behind the player.

Spoiler:During the Delta episode, if the player talks to Steven in the Mossdeep Space Center with a shiny Beldum, he will say that it reminds him of a trainer he teamed up with to battle Mega Rayquaza, who had a black Charizard, this is a refrence to Alain from the Mega Evolution anime special.

While playing through the special demo of the game, there's a small chance that the player will able to activate two secret missions. The first being an island with no wild Pokemon, but a double battle with May against Team Aqua or Magma. The second being a maze like island with a man who will give the player a Nugget.

Completing the second mission will open up more of Mossdeep City, including Steven's house.

Two old women could be found in the hot spring of Lavaridge Town in the original release of Pokémon Ruby & Pokémon Sapphire. They were removed in the Nintendo 3DS remakes, possibly because of the lewd nature of the scene. In Japan, it is common for people to bathe naked in hot springs, called "onsen", split by gender. In the original games' release, the male trainer was able to bathe with the old women, while an old man is also seen looking over the spring.

Latios and Latias were found to have Mega Evolutions in Pokémon X and Y before these forms were officially introduced in Pokémon Omega Ruby and Alpha Sapphire.

If the player visits a Pokémon Center on their birthday in any of the Generation VI Pokémon games, they will receive a special message wishing them a happy birthday.

In the Japanese versions, the Pokémon Center will additionally play a music box rendition of "Happy Birthday to You", which is replaced by a similar version of the Pokémon Center theme on subsequent visits that day. The international release omits the former song, only playing the latter even on the player's first visit. This is owed to the fact that "Happy Birthday to You" was still nominally under copyright in the United States, not officially falling into the public domain until 2016 after a three-year legal battle (the song was declared de facto public domain in 2015, but the final settlement was not issued until the following year).