Commander/Captain Rex stated the following as Order 66:
"Under this directive, any and all Jedi leadership must be executed for treason against the Republic. Any soldier that does not comply with the order will also be executed for treason."
BUT almost immediately after the issue of Order 66, Palpatine turns the Republic into the FIRST GALACTIC EMPIRE, so why are the Clones still following the order?
The order flat out stated "treason against the Republic" as soon as it became an Empire the order is no longer valid (as a new government took over and the leadership is no longer even a chancellery it's now an emperor) and the Clone's should no longer follow the order?
Yet the Clones still followed the orders as late as the Bad Batch