In the interview, Filoni revealed that the writer for the younglings story arc, Christian Taylor, came up with a solution for their issue. Filoni said:
“We knew that there was going to be a Jedi lightsaber master on board the ship, and we’re very strapped for assets when we build these things. The one problem we kept having — because initially, Yoda was going to be on the ship, and he was gonna be going back with them. I was like, ‘Wait a minute, I don’t care who’s attacking that ship. If Yoda’s on the ship, this is not going to be a problem.'”
That’s the issue with making your characters so powerful. You have to find bigger and bigger things for them to take on. By this point, Yoda is a badass. He’s a great teacher, but he’s also a great fighter. How do you find someone to take him down? They then discussed having another Jedi master on board. However, Filoni mentioned that they have Ahsoka there, and it just wasn’t going to work against the pirates because adding another Jedi meant they’d win handily. The balance would be off.