Within the game's data is an original cover of the song "Battle! Wild Pokémon" from Pokémon Diamond & Pearl. In addition, an early placeholder texture for score rankings features the names of numerous Pokémon characters.

Boss' sex is mistakenly listed as "Female" in the game's "Venus Mode Art Book".

Many Japanese players complained about the difficulty of the game, so much that Atlus released a patch enabling a new difficulty, Super Easy, which can be unlocked on the menu via a cheat code. The North American release was already patched.

In the Stray Sheep bathroom, you can find a poster of Teddie from Persona 4. The name Kuma is covering his face which is his name in Japan.

Inside the Stray Sheep bar, there is a doll of Teddie, a character from Persona 4.

Catherine's protagonist Vincent Brooks appears in Shin Megami Tensei: Persona 3 Portable. His name is simply "Man Drinking Alone" in the dialog bubbles but talking to him reveals his relationship issues and notes "it's nothing that [your character's name] needs to worry about" and even asks the player if they've ever had a dream where they're falling.

Before the release of Catherine in Japan, Atlus warned that "all gamers who share spoilers about Catherine will have nightmares and die".

When Catherine was released in America, the game came in two different sets of cover art. One set containing the Japanese cover and the other showing just the female characters' (Catherine and Katherine) faces. This was Atlus's answer to some stores wanting to "feature a cover that is more considerate of certain retailers' broader customer demographic."

In the "True Katherine" ending, Spoiler:it is revealed that the barmaid Erica was actually born a male under the name Eric.