The robot double from "Sonic and Sally" could very well have been a roboticized Mobian!
One of the early episodes had Robotnik capture an elderly Freedom Fighter known as Cat. By the end of the episode, Cat disappears. Because he is never seen again and he doesn't seem to have been roboticized, one can assume that Robotnik killed him.
Robotnik menacingly tells Cat he has "marvellous machines of all kinds, machines that can do things you would not believe!", which implies that Cat was tortured to death without even making it as far as the roboticizer.
There don't seem to be any humans aside from Snively and Robotnik. While it was planned for Mobius to be Earth After the End, Robotnik's backstory means that they weren't all wiped out. Did Robotnik kill them? Or is this the reason his SWATbotsresemble people?
Adding fuel to the fire, if they are robotocised humans then throughout the entire series Sonic and the Freedom Fighters have been killing, dismembering , and even WEARING humans!
In their defence, they probably don't know that they're humans, given that the main cast were very young when Robotnik took over. Which is still just as scary.
The chemical in the metal-eating balloons that appear in "The Doomsday Project" might have been harvested from the plants that appear in "Sonic Past Cool".