Creative Differences: Penders vs. Bollers got so bad, it ended with them both leaving the comic simultaneously. Which is why we have Flynn... whose works Penders steadfastly neglects to read, but swears to chuck in the Canon Discontinuity bin if he's ever re-hired. As of recent events, though, Penders returning is quite unlikely.
According to Penders, he claimed that it was the editor of the comic that forced him to bail, due to the fact that he kept on changing his stories, the final straw being the Mobius: 25 Years Later story. Of course, seeing as Penders has devolved into It's All About Me and Never My Fault, it's hard to tell if this is true or not.
Creator Backlash: The shipping wars got so bad that Ian has essentially sunk Sonic/Sally as a pairing with the soft reboot.
Executive Meddling: A large source of fan frustration. Sega doesn't like their characters getting hitched, for example, so you'll rarely see any romance with the video game characters after 2006 or so. Some game characters had parents in the comics but rarely addressed them as such due to editorial and company mandates, usually being cut off (for example, "My m-"). Eggman Nega has yet to make an un-obstructed appearance due to hang ups with Sega.
Due to a lawsuit between Archie and former writer Ken Penders, the characters he created were abruptly removed from the book in the aftermath of the Genesis arc. It's most noticeable in issue #244 where every echidna character Penders created was moved to another dimension. Off-screen. This led to a major case of Aborted Arc, due to the fact that many of the affected characters were integral to ongoing story arcs.
Likewise, elements created specifically for the Archie Sonic comics (and by proxy, it's precursor Satam) are not allowed to be used in other Sonic continuities due to the aforementioned legal embargoes. The closest exception was cameos of Satam and Adventures of Sonic characters in Sonic Spinball, which was a western produced Sonic spinoff to begin with.
Another odd mandate is that the writers are unable to call Mobius "Mobius" anymore (it's now referred to as "Sonic's World").
That's not to say there aren't straight examples, though. The Sonic/Image crossover is unlikely to be reprinted, and so is the first story in Sonic Live. Of course, these two stories were poorly received anyways.note The former due to it being a Back Door Pilot for Ken Penders' failed creator owned series (the villain of which was supposed to be the figure in Knuckles' ultimate destiny), misrepresenting the Image characters, and making the Sonic characters fictional in a reality. The latter due to the use of photos & characatures of real life children (Ken Penders' son & niece), an Idiot Plot, aexplicit statements the Sonic characters were fictional in an attempt to mimic the Arnold Schwarzenegger movie of "similar" name, and having the gall to state that Sonic's creation was mostly due to two white Americans with Yuji Naka being vaguely referred to as a "staff artist".
Promoted Fanboy: Several examples, most prominently current head writer Ian Flynn who was known as the author of a popular fan comic Other-M before getting hired as head writer.
Recursive Adaptation: The comic had already started to incorporate some plot elements from Sonic Chronicles, which itself had seemingly borrowed and modified some of its echidna lore material from the comic.
Screwed by the Lawyers: The ongoing lawsuit by Ken Penders has possibly led to the vast majority of the cast up and disappearing (too early to confirm, though). This is also telling in issue #243-244 where one comic ends with Sonic fighting Lien-Da and the rest of the Dark Egg Legion, then the next panel as Sonic coming to after being knocked out and asking where everyone went
As of #252, it seems that the entire universe has soft rebooted, with 256 establishing that the whole multiverse has been rebuilt: select characters like Sonic, Blaze and Eggman remember the original universe; others, like Naugus, remember them as vague memories; and there's those like Nu!King Acorn, who has absolutely no memory of the old world. The new universe has completely overwritten the old now, though, including memories, so the old world is now completely gone.
The aforementioned embargo on using characters or elements from series like Sonic X due to copyright issues.
Shrug of God: When asked about the fate of Robotnik's parents, Flynn posted two ideas. One was that Robotnik "did away" with them. The other was that they migrated to the United Federation. In either case, the writer leaves it up to the reader.
With the recent reveal of Sonic Boom, there have been questions asked as to if this would be incorporated into the comic in anyway. So far, the only answer has been "No comment."
While Ken Penders' characters can't be used, there has been no comment on whether or not characters from other writers (besides the current team) can make an appearance now, though it seems it may not be the case. Also, while Scourge was technically introduced by Penders as Evil Sonic, whether or not being an evil version of Sonic means he can still appear is unknown even by the current writers. However, due to Ken claiming that he created the concepts of evil Sonics and a multiverse for the comics, Archie's not going to have either to avoid any more legal issues.
What Could Have Been: The original plot for "Endgame" really did involve Sally's demise — her apparent restoration later on was to have been a robot double, the truth only slowly coming out later as "Sally" began to act increasingly suspicious and out-of-character.
Ken's stated that some of the original ideas for the Princess Sally miniseries included a roboticized Queen Alicia ruling over her own subjects as a threat to both the Freedom Fighters and Robotnik. Another was a Thelma and Louise type story with Sally and Bunnie. Sega vetoed both of these ideas, wanting to use only Sally and Robotnik. This is what led to the Substitute Freedom Fighters and Geoffrey St. John.
Regarding the Source of All, one of the ideas that Ken was brainstorming with a friend of his was that the Source was actually an AI made out of a pool of nanotechnology, from either the past or the future, that was so advanced as to be indistinguishable from magic. However, they never figured out what it's motives were before it was nuked.
Both Karl Bollers and Ken Penders have made public their plans for the comic had their employment at Archie continued.
Ian Flynn originally intended to have E-123 Omega off Tommy Turtle, but Executive Meddling had that changed to the Egg Fleet. In fact, Executive Meddling kept Omega from appearing in the comic for some time since Karl Bollers tried to put him in. It wasn't until issue 3 of Sonic Universe that he made an appearance.
One of the biggest cases of this was the Endangered Species arc. Part one had font that was obviously put in at the last minute to keep from referring to certain characters by name, while the rest was completely rewritten to remove them altogether. The arc was controversial at best as a result.
Ian's already given a little bit out: Endangered Species was originally planned to have a happy ending.
Flynn has also gone on record to say that the early implied romance between Tails and Barby Koala (of the Downunda Freedom Fighters) is "completely one-sided and kind of creepy", (most likely due to the age difference, with Tails being around 11-12 and Barby appearing to be in her late teens) and that as long as he's on the comic it's not going to happen.
Word of Gay: Ken Penders got around the CCA somehow by hinting at one of the characters in the "Mobius: X Years Later" storyline being gay... and somehow doing this while showing the life partner, threading the relationship into the text. Once fans started searching, it became obvious (and confirmed by Ken), that the hinted couple was Rotor and Cobar, the latter an echidna scientist from the Dark Legion.
Current writer Ian Flynn has organized his own message board, where he and other creators interact with fans and answer their questions. His predecessor, Ken Penders, also kept up a message board while he was writing for the comic, which is still active and occasionally talks about the stories that he had planned for the series.
The events of Sonic the Hedgehog (2006) occurred in the comic as they did in the game, including the Cosmic Retcon. Soleanna was mentioned once by the Babylon Rogues and issue #246 has a brief appearance of White Acropolis, those are the only nods towards Sonic '06. The Complete Sonic Comic Encyclopedia describes it in more detail, including entries on Iblis, Mephiles, and Solaris.