The Nintendo Switch remaster of the game adds a new five-chapter storybook similar to what the first game had, which tells the story of two identical twin sister Lumas named Mari and Lu. In the events of this story, it's revealed that Lu would grow up to become Lubba, the captain of Starship Mario, which subsequently revealed that the character had been retconned to be female. Previously, Lubba's gender had not been consistent between the original game's localizations and other appearances, a discrepancy that was not widely known up until the release of the Switch version.

In the original Japanese release of the game, Lumas were not referred to with gendered pronouns, and in a developer interview published in the original game's Japanese guidebook, producer Yoshiaki Koizumi claimed to not know what Lubba's gender was, simultaneously referring to her with male pronouns and comparing her to a grandmother or aunt (depending on the translation) to the surprise of the interviewer. The original English, French, and Italian localizations designate Lubba as male, while the original Spanish and German localizations designate Lubba as female. In all versions of the game, she is voiced by a male voice actor, Scott Burns, and both the original English and Japanese websites for the game use male pronouns. Prima's English eGuide for the original game appears to avoid using pronouns for Lubba entirely.

This confusion extended to Lubba's trophy description in Super Smash Bros. for Wii U, in which the English release calls Lubba male, but the Japanese release does so while comparing the character to "an older lady from a working-class neighborhood."

The Bowser statues that shoot lasers out of their mouths are referred to in the game code as "KoopaStatueVomit".

The Whomp King, the boss of the Throwback Galaxy, will recite his original speech from his first encounter with Mario at Whomp's Fortress in Super Mario 64. If you lose the fight and then try again, he will start to recite the speech again, and then stop himself declaring he's tired of it. Excluding Bowser and Bowser Jr., the Whomp King is the only standard boss in the game with dialogue. When you deal the final blow to the Whomp King, he makes a unique face that cannot be seen normally because he is lying down when defeated.

The Toy Time Galaxy theme in Super Mario Galaxy and the Supermassive Galaxy theme in Super Mario Galaxy 2 may both be based on "Mario Syndrome", an alternative dance remix of the Super Mario Bros. overworld theme by Japanese act Bonus 21 that was released as a 12" and cassette single in 1986. Both themes feature similar instrumentation and compositional choices as "Mario Syndrome", though foregoes the 1986 song's dance elements.

Twisty Trials Galaxy in World S has an area which is the exact same as an area in Super Mario Sunshine. The level "Spinning Spinning and Spinning," is the same as the trial area in "The Secret of Ricco Harbor".

During development, characters such as Pikmin and Donkey Kong were planned to cameo in the game. However, Miyamoto didn't allow it, feeling that the Pikmin especially wouldn't fit well within the game. Years later however, Pikmin would make an appearance in the 2026 film "The Super Mario Galaxy Movie".

When you collect x777 or x7777 star bits and talk to the Captain, she will say "Hey, you have 7777 star bits! How Lucky!". Also if you have x9999 star bits, she will say "What happens when you get 9999 star bits? Something nice I bet!".

In both games, if you happen to have 9999 Starbits on-hand, all coconuts will turn into watermelons.

It is possible for Mario to get a Game Over during the game's closing credits. Finishing the game with 120 stars, a Bee Mushroom will appear in the Tall Trunk section of the credits. Collecting it and flying to the right in the Freezy Flake section of the credits, it's possible to get enough height to bypass the top boundary, thus resulting in a Game Over. The credits will roll, but are invisible behind a black screen.

The Japanese, European and Australian versions of the game came packaged with an instructional DVD manual, explaining the basic controls, as well as showing advanced play. It was made because Super Mario Galaxy 2 would be more challenging than its predecessor. It's unknown why a DVD was never packaged for the American release.

The Diggas seen in the E3 2009 Trailer had a different design than those found in the Spin Dig Galaxy in the final version. Their eyes were positioned on their sides, rather than on top, and their bodies were rounder, making them look more like yellow Bullet Bills.

The Boss Megahammer was at one point called Mallettoid, and was referred to as such in demos.

Inside the game's files is an unused animation for King Lakitu. It shows him being hit so hard that his glasses fall off, causing him to search his face for them. However, the animation appears unfinished, as his fingers do not move, and his expression does not change.

Yoshi was originally planned to appear in Super Mario Galaxy, and was featured in proposal documents for the game from 2005. However, he was removed due to the developers thinking that "it would've been too much all at once." They said that, "if you're going to put Yoshi in a game, he has to be a main element, but [Super Mario Galaxy] had spherical land forms and gravity shifts and lots of elements that were entirely new" and, "Even if we had used him, we might have only been able to use him on a single stage."

Despite this, it was decided early on in the development of Super Mario Galaxy 2 to include Yoshi in the game, because his control scheme could act as a new main element of a new game and a "multiplication" of the elements from the previous game. The Wiimote controls for Yoshi were also formed early in development, with Shigeru Miyamoto taking pride in the tongue pulling mechanic used for eating fruit, fighting enemies and flipping switches, saying it "isn’t like anything you've ever experienced before." The rest of Yoshi's controls were shaped based on internal feedback from "everybody's love" for Yoshi, listing the development team, Mario Club Inc., and Nintendo of America as primary influencers for what the image of Yoshi should be, but tried to avoid making him too powerful. The developers also had composer Kazumi Totaka record new voice lines for Yoshi for the first time in ten years, and was reported as feeling "a little uneasy" and worried that Yoshi would sound like he had aged, but these were not concerns to them and the recordings were used in the game.

Yoshi can be found at Bowser's Galaxy Generator. If you successfully bring him to the end, he will wave goodbye to you as Mario goes up the flag leading to the final boss.

Super Mario Galaxy 2's internal disc ID is titled "Super Mario Galaxy More". This could suggest that Nintendo originally made the game as an expansion pack, rather than a true sequel.

Super Mario Galaxy 2 was the most pirated Wii game for 2 years running (2010-2011) with over a million downloads each year.

Yoshi's house can be found in World 1, Sky Station Galaxy. If you select the first mission and go up to Yoshi's house, there will be a sign in the front that reads: "Hello, friend! Please go around back! -Yoshi" If you then quit the level and then select the third mission and read the sign, it will read: "Hello, friend! Please go around back! -Yoshi the space dragon"

There is a level called the Throwback Galaxy. This level is the same as Whomp's Fortress from Super Mario 64 with a few changes and improved graphics. In the level, a Bob-omb Buddy mentions that Mario looks familiar, most likely referencing that he remembers him from Super Mario 64.

In the beginning of Shiverburn Galaxy, you can see odd, alien figures in the backgound. The name of the image in the game's files is "HellValleySkyTree." This same background re-appears in one portion of Grandmaster Galaxy.