Clearly not all of the Jedi had command over the Clone Troopers. What position did a Jedi have to attain within the Order to be able to command Clone Troopers?
As we learn in Star Wars: The Clone Wars, any Jedi who has attained the rank of Padawan can command Clone Troopers. That doesn't mean that they can countermand the orders of a more senior Jedi or a Jedi who is acting as a General in Command. Padawan Ahsoka discusses this situation with Commander Rex.
"Thank you, but General Skywalker thinks they're fine where they are."
"But they need cover."
"They also need range."
"What if I gave you an order to move the cannons? You're a captain, and I'm a Jedi, so I technically outrank you, right?"
"Technically, you're only a youngling."
She looked as if she was going to continue, but she stopped of her own accord. Rex didn't need to interrupt her. It was as good a time as any to do what a fellow clone captain called picturizing, a lovely mild word for putting someone in their place.
"Look, littl'un," Rex said, "why don't I explain how things are in the real world?"
Ahsoka bristled visibly. Rex had never served with Togrutas before, so he wasn't sure what was normal for their youngsters. But he knew how a Jedi should behave, and she wasn't doing it.
"I still think..."
This time, he did interrupt.
"Are you scared?"
"Well, you should be. Because if you're not scared in a war, then you haven't grasped the severity of your situation."
Rex sat down on a chunk of masonry so he was at eye level with her. He preferred training by example, but that would have involved letting her get blown up, and he had to cut her some slack. She was just a kid, full of a kid's weird mix of uncertainty and overconfidence about a brand-new rank, as if it would stop a blaster bolt if she brandished it enough.
"I take my orders from General Skywalker. It's called the chain of command, and it matters, because we all have to be clear who's in charge, or else we'll be running around like nuna. And you take your orders from him, too, because you're his Padawan. With me so far?"
That defiant jut of her chin had receded a little.
"Want to learn the most important things about being a soldier? I mean the things they don't teach you at the Temple."
"How would you know what they teach Jedi?"
"By watching you ..."
Ahsoka dropped her chin another fraction.
Rex ratcheted back a few notches. There was no point rubbing a kid's nose in it. You had to climb down with them.
"One," he said. "Orders. You follow orders. They keep you alive. Two, you're part of a team. We look out for our buddies. I cover your back, you cover mine. And three, an officer rank doesn't give you automatic respect. You earn it. It's not just Skywalker's rank that makes us give him one hundred percent. It's because he treats us with respect, and he puts himself on the line with us."
Warning: Mild Spoilers in this video beyond 00:15.
little late on this but Im going to say what u probably have already heard padawans can but only to a certain limit and if Ahsoka wasn't there Captain Rex would be Commander Rex if that helps and some padawans probably couldn't if their masters felt they couldn't and usually older jedi who are generals who can command troopers