A popular belief within the Friday Night Funkin' fandom is that the game's main protagonist Boyfriend used to be in a relationship with Pico, the main protagonist of Pico's School and the opponent of Week 3. This gained so much traction that Tom Fulp (the creator of Pico's School) jokingly said it was "official Pico 2 canon". Programmer NinjaMuffin99 initially claimed this was just a joke, but later changed his mind and confirmed it was canon. The cutscene for the song "Stress" alludes to this, as Tankman mockingly refers to Pico as Boyfriend's "sexually ambiguous, angry little friend."

On April 1st, 2021, Tom Fulp updated Pico's School as an April Fools Day joke, with this version ending with Pico revealing to Cassandra that he and Boyfriend are dating and that everybody in the school accepts them. The next day, this version would be released as a separate game called Pico's School: Love Conquers All, being set in an alternate timeline. Given that the game portrayed Pico and Boyfriend's relationship in a positive light, some fans have taken this as a sign that Tom Fulp approves of the idea that they were at one point a couple.

According to animator PhantomArcade, Nene's redesign for the game went through numerous changes that ultimately did not go through. Additionally, he was the only person on the team involved with Nene's redesign.

On December 6th, 2020, an Itch.io user revealed that the game files contained a sprite sheet for Lucky Boy, the titular main character of the 2021 animated short film "LUCKYBOY" as well as an associated audio file called "vidyagames.ogg". This file was actually a low-quality version of the song "Video Games" by the band Black Out Band with a song length similar to that of the game's official songs. Upon this being shared, the game's creator and co-director ninjamuffin99 revealed these were added to the game by his friend Brandy and that they would both be removed as they were not meant to be part of the final game. Lucky Boy's animations were made by Dylee Dee, the 2D animation director for the "LUCKYBOY" short, with some of them (such as the tumbling animation) being used in the film.