- Creator Breakdown: A literal example, for according to this, Jamal Peppers, who drew parts one through three and most of four, was hospitalized before he could finish the last few pages of part four. Ryan Jampole stepped in to finish the pages for him so things could go according to plan.
- Development Gag: In Sonic Universe #51, Doctor Light is seen working on Bond Man, who he's "been putting off building since the original line."
- In the Off-Panel comic for Sonic Universe #54, Bass announces that he and Metal Sonic will combine their power, resulting in... a musical act. Mega Man thought they were going to fuse together.
- Keep Circulating the Tapes: A consequence of Archie losing the Sonic license to IDW, this crossover cannot be reprinted, and due to Sega and IDW wanting to move on from the Archie Sonic material as of this writing, it looks pretty unlikley it'll get reprinted at all.
- Executive Meddling: A rare case where a crossover is used to execute the meddling. Namely, all of the Sonic characters created by other writers pre-Sonic #160 or associated too strongly with them can't be used anymore. So the Cosmic Retcon at the end doubles as a way to get them out without requiring another story or just killing them all off.
- I Knew It!: Quite a few fans guessed correctly that Robotnik and Wily were going to have a nasty falling out.
- Name's the Same: The Roboticized Master, Shadow Man, and the actual Shadow Man from the Mega Man franchise. Lampshaded in Part 6, where Eggman announces he'll send Shadow Man to intercept the heroes, Wily asks which one. After a Beat Panel, they agree to send both. Then, in Part 7, when faced with them both, Sonic has trouble giving directions to Mega Man about who to attack.
- An example involving another occurs later on in part five with there being now two green Sega robot characters named Vector Man. Also lampshaded in Part 6, where the character's name reminds Sonic of a trash collector, which was the job of the original Vectorman.
- Milestone Celebration: As the 250th issue of Sonic the Hedgehog, Part 9 primarily features a Big Badass Battle Sequence so massive that Ian Flynn described it as something along the line of "the moment I'll get death threats from the art team." It shows. Also, it includes a reprint of the ending of Sonic the Hedgehog #229, the end of the first usage of the Genesis Wave. The "Off Panel" comic is all about the milestone, for good measure.
- Then there's the fact that Part 4 was the 25th issue of Mega Man and immediately prior to the crossover was the 50th issue of Sonic Universe that introduced the version of Metal Sonic that would show up in the crossover. Milestone celebrations all around!
- Shout-Out: Sonic states that Vector Man's name reminds him of a trash collector.
- What Could Have Been: Ian Flynn was originally planning to have Bass and Metal Sonic combine into a single entity, but this idea was shot down early on. The weakness of said boss would've been Rouge Woman's Black Wave, the only time it would've been used.
- According to Spaz in the first paperback's special features, the basic idea of having Archie Sonic crossing over with Mega Man dates as far back as when Dreamwave's Mega Man was running, but the deal never went through. Not much is known about this version of the crossover, though Spaz said all that really got carried over to the final version was the basic idea of a "sneakers and helmet" image that got used in one of the teasers.
Trivia / Sonic the Hedgehog/Mega Man: Worlds Collide