“Knuckles is the last of his kind, so no Echidnas, *ANGRY SCREECHING*” pisses me off because that’s a plot-hole in and of itself.

Someone had to have given birth to him and unless there’s been centuries of inbreeding that means he couldn’t exist without a decent population of his species at least up until his parents. At that point you could infer (though unlikely) some cataclysmic thing wiped out literally every single living one but him.   

I like to call this selective suspension of disbelief.