The story section of Sonic Underground's manual has numerous inconsistencies with the plot of the show it's based on, though are still featured in early production documents. These include:

• Robotnik at one point being referred to as "Sheriff Robotnik", likely a reference to the Sheriff of Nottingham from the legend of Robin Hood. He does not bare this title in the show itself; early leaks to the show's plot prior to release also reference his role as a sheriff, suggesting it was a scrapped concept from early on in development.
• The Oracle of Delphius being banished to the Frozen Wastes by Robotnik and passing away from unknown causes sometime after, telling Sonic how to reunite with his siblings in his dying breath. While the Oracle does take up residence in Ice Cap in the final show, he was not banished there, nor does he ever die.
• The Medallions being stated to be golden, but in the final show they bare a more silver coloration. Another detail stated in the manual but not in the final show is that they each possess three notes engraved into them.
• Robotnik's given motive for finding Queen Aleena is so that he can marry her and make her his consort, as he believes that by doing so he can become the rightful ruler of Mobius. While not his overall motive in the final show, the episode "Wedding Bell Blues" did use a similar premise for its plot.
• While not in early production documents, the game's manual states that it ends with Sonic, Manic and Sonia reuniting with their mother, which never actually happened in the original show, making it the only piece of Sonic Underground-related media where this goal is actually accomplished.