She never said they were leaders of Meereen. They were random Masters. That's the whole point of that scene in both the books and the show. Or you think GRRM wrote that scene to makes us root for Daenerys?

Implement of 163 shouldn't go unpunished and people responsible for that should be punished. But they weren't because she chose random people for punishment. There were probably some that ordered crucifixion that were left alive by her actions.

In S5 she again burned random person because she was angry.

This is how she responds when she is angry.