Rex and about half his loyal troops formed the 332nd Battalion within the 501st to fight under Ahsoka’s leadership.
So it’s highly possible that when Order 66 popped off, all your favorite clones were caught up in the Siege of Mandalore.
Safe to assume that the 332nd was formed by Ahsoka’s favorites within the 501st. And her favorites tended to be the focal point of TCW episodes.
Meaning more than likely, Ahsoka’s troops had guys without chips and guys with chips. So when the Order came down they weren’t just hunting Ahsoka or Darth Maul.
They were hunting their brothers. Guys who already lost Tup and Fives to circumstances they couldn’t understand and yet drove them to honor his legacy with surgeries.
Rex has gone on record saying he didn’t betray his Jedi general. But since Filoni and Hidalgo confirmed that Rex would’ve been in Ahsoka’s unit during the Purge, and seeing as how there’s no bad blood between them when we see them in Rebels…
Rex and god only knows who else, fought their own to save their Commander and then went into hiding.