Because the developers were still experimenting with Double Battles where the player teams up with an NPC ally to fight two NPC opponents, this lead to a glaring oversight during the battle where the player joins with Steven Stone to battle Maxi and Tabitha where, during the battle, Steven's Level 42 Metang can actually gain a substantial amount of EXP simultaneously with the player's own Pokémon. This essentially means that, with careful manipulation, the player can have the ally Metang get enough EXP to grow to Level 43. This so far is the only instance in the entire Pokémon main series where, in a non-scripted battle, an NPC's Pokémon can gain EXP and level up.

The Team Aqua/Magma Leader Battle theme music featured in Pokémon Ruby, Sapphire and Emerald is based on the Shionchou boss battle theme music from Game Freak's Super Famicom game Bushi Seiryūden: Futari no Yūsha. The themes were written by both games' composer and Game Freak co-founder Junichi Masuda.

When traveling on the cable car, there is a 1 in 64 chance for an NPC to appear in the background - a hiker, a camper, or a picnicker. However, there also exists a 4th NPC which never appears due to a faulty line of code. These include a Zigzagoon in Emerald, and a Poochyena in Ruby and Sapphire

In the Japanese release, the player is able to use Dive on the deep water tiles in Team Aqua's hideout due to a programming oversight. Because these tiles were never intended to lead anywhere, diving in them simply teleports the player back to Petalburg City, the lowest-indexed map location in the game. In the international release, this error is fixed by disallowing the player from using Dive in the hideout.

This glitch is not present in Pokémon Ruby & Sapphire, because in those games, the entrance to the hideout is no longer accessible after obtaining the Mind Badge, which is required to use Dive in the overworld.

The games' most prominent subplot focuses on the conflict between Team Aqua and Team Magma in their efforts to gain control of the legendary Pokémon Kyogre and Groudon to change the climate in response to the effect of humans on the environment in order to create expanded environments for sea and land Pokémon respectively. Although it has not been confirmed by the developers, this subplot may have drawn direct inspiration from a real-life controversy that was a prominent issue in Japan at the time of the games' development and continues to be. The Isahaya Bay land reclamation project on the Japanese island of Kyūshū, which the Hoenn region is based on, aimed to expand the available farmland in one of Japan's last wetland habitats. This lead to fierce political conflict from environmentalists who argued that the project would cause long-term damage to the wetlands and the marine ecosystem of the area through agricultural runoff released into the sea, and from reclamation activists who argued that Kyūshū needed the land as Japan has very little arable land already and needs to produce enough food to feed its increasing population and keep up with rapid industrialization. The concept of Team Aqua and Team Magma draw striking parallels to each side of this issue (i.e. reclaiming land where there used to be sea and protesting to reclaim sea where there is now land) while being written as cultic villains akin to Team Rocket from past games without distinct arguments to their positions. This causes these parallels to be obscured and emphasizes the personal gain of expanding, or reducing land for the sake of certain land, or sea Pokémon to be won out from the conflict with little to no regard for humanity.

In Pokémon Emerald, the unified story featuring Kyogre and Groudon both being pacified by the presence of Rayquaza, a Pokémon heralding from the sky which in many religions and mythologies is where powerful gods and deities live, hints that a divine compromise between civilization and nature is the necessary solution, with how Hoenn is presented in the final game through the coexistence of different environments, humans and Pokémon being the result. This suggests that the preservation of Isahaya Bay while allowing for land reclamation elsewhere is the compromise this subplot is trying to get across.

The order that your rival Brenden or May sends out their Pokémon during battle is determined by which gender they are and, thus forth, is also determined by which gender the player chose for their own character before their adventure started. However, for reasons unknown, this only works if the starter the rival choose was Treecko.

The player can completely softlock their game if an extremely complex and absurd series of actions are undertaken, forcing them to have no other choice but to start a new game. Specifically, if this is done, then the player will be stuck at either the Pokémon League building, Pacifidlog Town, Dewford Town, or Sootopolis City with only an Electrode that only knows the move Selfdestruct.

This is not possible in the Generation VI remakes.

The Mirage Tower, exclusive to Emerald, may be a reference to a tower with the same name which appears in Final Fantasy. Both appear in a desert, only appear under certain circumstances, and contain a spiral-shaped dungeon.