This is gonna be a long one (it's Sonic Prime)
First, we never get an explanation of what caused Rusty to turn evil.
Second, Dread is way too protective over that Shard.
Third, I get why Shadow and Sonic are fighting later in the show but Shadow has no reason to be fighting Sonic in the first fight.
Fourth.... *sigh* Nine's betrayal.
Fifth... OK, I get that the Chaos Council are evil, but you'd think that they would've gone back and saved Rusty instead of just leaving her.