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.
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.
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.
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."
Torch the Franchise and Run: It's not hard to see that the "Countdown to Chaos" storyline was pretty much Archie going "See this old continuity, Penders? Buh-bye."
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.