Order 66 was clear: Execute Jedi for their treason against the Republic.
But, after receiving Order 66, Rex also ordered his troops to kill Maul. Why? Maul wasn't a Jedi in any way.
I had asked a similar question for Ahsoka: Why did Rex want to kill Ahsoka after receiving Order 66?
In the case of Ahsoka, there's a grey area, but Maul was never a Jedi or an ally of the Jedi Order.
Why did Rex order his troops to kill Maul?