So will they ever explain what happened to the human Foot Ninjas
 

I mean where did they all go when the Foot Bots came? Their disappearance leaves a lot in question.

I mean they couldn't be fired cause then they would go to the FBI and say something like "Hay "Murica? You have Japanese crime lord in New York. EL OH EL!"

And they can't be disposed of cause sooner or later their bodies will be found and the cops will question why a bunch of Japanese dudes are dying

And they could go back to Japan, but what's there for them anymore?

Unless the footbots are not as entirely robotic as they look....

I'd imagine Shredder sent back the Japanese members, while the Bradford recruits got nixed one way or the other.

I think it was sort of implied that the Human Foot soldiers were all executed. Shredder does threaten his followers with bodily harm and dismemberment for their failure.

Typically the Turtles knock out all the Foot Soldiers from season 1.

In Pulverizer returns, the Shredder tells Dogpound that he was promised 100 skilled warriors, but the Turtles have decimated them and the ones who remain are not worthy of calling themselves part of the Foot Clan. So if the Turtles aren't killing the Foot, then someone involved with the Foot Clan are killing the Foot Soldiers.