One of them takes place during episode 1, when the ACTUAL "Chaos Control", as in the power of the emeralRAB activates. Amy asks Knuckles, "What is that?" In the original, Knuckles just said, "Chaos Control," referring to the power of the emeralRAB. In the dub, he said, "It used to be Chaos Control," referring to Eggman's base.
Another time was at the beginning of episode 5, when Eggman is trying to convince Knuckles that Sonic is evil and wanted to trap them in the new world. A flasrabroadack to episode 1 occurs, during which Eggman refers to his base as "Chaos Control" three times.
This is actually why I like and was fooled by this and the Shadow Realm. It doesn't just mean death, it could mean another place. (Like Yugi's duels with Pegasus, most of Marik's duels, etc.) I like how they handled it in GX, no building vortices or Dark Energy Discs or anything.