According to director Tetsu Okano, the spritework for Stage 3: "Astro vs. Atlas" was entirely done by artist Tomoharu Saitō, who worked on stage and character sprites in different capacities. Okano credited him for helping to save the game under a tight schedule and for mediating Hitmaker's professional relationship with Treasure, but his efforts came at a personal cost. One night during dinner towards the end of development, Saitō revealed to his colleagues that his legs had become swollen, numb and white. They told him to immediately go to a doctor, but he insisted that he wanted to continue working and treated it "as if it were no big deal". According to Okano, it was specifically his work creating the graphics for Stage 3 that kept him from going to a hospital sooner.

At the game's launch party, Saitō announced that he had been diagnosed with osteosarcoma and that one of his legs had been amputated and replaced with a prosthetic metal rod, stunning the development team. Despite this, he shrugged it off saying "legs aren't necessary in the [game and illustration industries]." Okano stressed in his recounting of this event that despite the tight schedule, Saitō was one of several "mercenaries" working on the game who could have taken breaks whenever he wanted, and that the development team as a whole were not forced to work. Okano believed that Saitō hid his illness to maintain "his own self-respect as an artist" and that the game "is filled with [Saitō's] soul", but clarified that he did not think that the game was good "because it sacrifices someone's lifespan". Okano felt that he owed a debt to Saitō for the rest of his life for "[robbing] him of his leg", but they would never work on a game together again. Saitō continued to work, but the cancer recurred and metastasized into his lungs, leading to his death in 2006 while working on the game Culdcept Saga.

The game went through massive changes when it was ported from Japan to the US. The Japanese version only has Easy and Difficult difficulty settings. The International versions removed these in favor of Normal and Hard, with Normal as a re-balanced version of the original Difficult. The international versions also add a health meter for the bosses, language selection, a couple new enemies, adjusts some of the level layouts, and fixes some of the slowdown.

There is a secret room in Stage 6: "Lost World" in which a unique enemy can be found. It appears to be a white octopus with a pink ribbon, and will drop a health pickup if attacked. This character is called "Ebiinu-kun", and was created by the game's director Tetsu Okano. Ebiinu-kun was later featured in a manga he wrote and illustrated under the pen name "Ichizo Sorge" in 2008 called "Zolman Ebiinu-kun" (ゾル漫えびいぬ君).

The music that plays in the last scene of the game is the same music that plays in the last cutscene in Gunstar Heroes, also developed by Treasure.