In an early version of the game, a pie weapon was planned to be included that allowed Bubsy to throw pies at enemies. However, this weapon would ultimately only appear in the Game Boy version.

A port of Bubsy 2 to the Sega Game Gear was planned and seemingly completed, but never released. In the surfaced screenshots of the game's prototype, it appears to be a fully colorized version of the Game Boy version (playing the Game Boy version of Bubsy 2 on a Super Game Boy will give the graphics a slight red tint).

While Bubsy 3D is often considered to have killed the Bubsy franchise until its revival in the late 2010s, the franchise was not killed by Accolade as one may expect. Accolade wanted a new installment titled Bubsy 4 (Bubsy in Fractured Furry Tales not being considered part of the franchise's official numbering) after Bubsy 3D's release, but series creator Michael Berlyn was the one who pulled the plug on the franchise, believing that Bubsy 2 and Bubsy 3D had dealt too much damage to it:

The working titles for Bubsy 2 were "Bubsy 2: Still No Pants!" and "Bubsy 2: Lost in the Amazatorium".

There is a rumor that claims that Rob Paulsen, the voice actor who provided the voice for Bubsy in Bubsy 2, Bubsy in: Fractured Furry Tales, and the 1993 Bubsy cartoon pilot hated the character and regretted taking the gig. However, Paulsen has stated that he does not regret his role in the Bubsy franchise and would do the voice again for future Bubsy projects if paid to.

The late Michael Berlyn, who created Bubsy, has claimed that the designer of Bubsy 2, Cyndi Kirkpatrick, vehemently hated Bubsy to the point of sticking pencils through the heads of rare promotional Bubsy dolls, hanging them from nooses and covering them in fake blood. Berlyn claimed this hatred affected the quality of the final game for him in that "the art wasn't quite right, the feeling wasn't quite right, and they did some weird things with the secondary characters, and the biplanes, you know, nothing really worked for me."