During the episode where Cosmo and Chris are captured, Sonic transforms into a new "dark form." While this may seem like an Ass Pull at first, one must take this into account — they are surrounded by (duplicate) Chaos Emeralds. The Chaos Emeralds have two types of energy — positive and negative. Positive is activated by those pure of heart, while those who are consumed by rage will use the negative side. When thinking of Sonic's state of mind, he was quite angry, no? That wasn't some kind of hidden demon locked within his heart, or some new kind of technique he had learned — Sonic had just used the negative energy of the Chaos Emeralds!
Throughout the entire Shadow Saga, Chris continually reminds Shadow of Maria and acts as somewhat of a Morality Pet. You might think it's just an excuse to give Chris a ton of screen time again because of his intended status, until you realize that Chris and Maria are more similar than you think. They both have done reckless things to help Sonic and Shadow respectively (to the point that it cost Maria her life), and even though Chris has some bratty moments in the show, for the most part he's still a kind, idealistic kid like Maria was. That, and Maria died at age 12 while Chris was 12 at the time of season 2 (or season 1 part 2).
The production team's choice to use The Shining Road as Amy's credits song in the first ending sequence makes more sense when you realise it represent's Amy's crush on Sonic as being a doomed, one-sided attraction. It becomes even more heartrending when it's used to represent Tails and Cosmo's relationship in the finale.
At the end of the third season after Cosmo sacrifices herself, the seeds of her species are spread across the galaxy. Now then, take into account that we don't see where most of them land. In fact, we don't see where any of them land. Let's also take into account that it was shown that Cosmo Grew from a seed into a small baby. This means That all of Cosmo's seedling would develop into babies.
That's probably why there's so many of them in the first place: statistically, some would have to land somewhere on a hospitable planet. Some of them would develop in the wild, without any civilization. Or worse: end up in a sun, or something similar.
Speaking of Cosmo, imagine what would have happened if the tracking device that allowed the Metarex to spy on Sonic and the others through Cosmo's eyes and ears was actually removed just like how Knuckles suggested in the dub - basically, Cosmo would have ended up blind and deaf for the rest of her life. The fact that Cosmo is eight years old at the time doesn't help matters.
And why did Cosmo not remember about how exactly she escaped the destroyed space colony? It's very likely that the Metarex modified her memories in one way or another...
All the way back in the first season's Episode 12, during the attack on Eggman's base, numerous fighter jets are seen being shot down or otherwise destroyed; while many of the pilots do eject, some scenes show a notable LACK of ejections. This, combined with the missile and laser hits seen taken by guided missile destroyers and the ensuing explosions, indicates that plenty of airmen and sailors are dying in a 4kids-aired show—something that might not exactly have been clear to younger audiences when first aired outside Japan, as the focus was on Sonic, not the background military forces.
The Dark Super Sonic sequence gives Sonic fans outside the UK a brief taste of what could happen to Sonic if he tapped the negative power of the Chaos Emeralds, in a way that is more descriptively chilling than Fleetway's Super Sonic incarnation. The dub adds in some wicked laughter that would not be out of place on Fleetway Super Sonic. It's also very much like the form of Darkspine Sonic that is seen when Sonic loses his cool during the final boss battle of Secret Rings, full of berserk anger and focused on destruction, and also gives insight into how Perfect Chaos destroyed the powerful ancient Echidna empire when he attacked them in retaliation for murdering his Chao friends, and why that event scarred so many ancient civilizations, that warnings about the power of the Chaos Emeralds and prophetic murals can be found in ruins in South Island, West Side Island, the Mystic Ruins, and even on Angel Island itself (This is also why the seventh Chaos Emerald was sealed away in West Side Island, and why the Master Emerald was placed outside of man's reach on the Floating Island, with Knuckles as its last Guardian). Remember Tikal's words: "Chaos is power, enriched by the heart." However, if that heart is full of anger and desires for destruction, then the only thing that can happen is a calamity.
The dub claims the GUN "took Maria away" following the ARK massacre. As they almost certainly did not have the ability nor inclination to treat her condition, Maria died a slow and painful death. And the soldier who originally shot her seems to be aware that he sentenced her to this fate...
Chris decides to throw himself into a portal at the beginning of Season 3 to try to help Sonic out. A portal that is, by the context given, untested for this purpose. And he words it like one's final will before they die, basically making it sound like he has absolutely no idea if he'll even succeed or not, which is even more opaque in the Japanese version. As far as anyone knew, Chris just threw himself into a warp to Sonic's dimension to continue being with him at complete neglect to his home life that he had grown into, and potentially died for it with absolutely no way to confirm if he was still alive. What the hell, Chris?
