Was it ever explained why the Clones did not kill Anakin, a Jedi as far as they are concerned. Or the Jedi who later became Inquisitors? Was it something in the inhibitor chip, or something else?
I don’t think it has been explained. I think is one of those things the writers probably want us not to think too much about? I am probably wrong, or forgetting an important episode, but I can’t remember an explanation.
In the final season of The Clone Wars, after Order 66 I think there is a mention of clones saying something about Ahsoka still being considered a Jedi, which is why they turn on her too? (despite her leaving the Jedi some time before.)