It might have been a Heart of the Tiger thing - there's no indication that they knew about this order prior to being told to execute it.Delance said:The odd thing is how the Clone Troopers apparently were aware of the order to kill the Jedi, and the Jedi could not figure this out. It should be easy for the emperor to keep a secret, but not to all those clones.
The price of not reading the fine print, I guess - had the Jedi reacted to news about the secret army in episode 2 in a manner more cautious than "a secret army, eh? Can we use it?", things might have turned out a bit differently.