To expand on my comment, I believe the correct fix is not to sort Meta sites below their parent, but to remove Meta sites from the list entirely. Unless that overcomplicates some implementation details, I have never seen the need to migrate a question from Software Engineering to a meta site other than Meta Software Engineering or Meta Stack Exchange. If anyone has a use case, I'd be interested to hear about it.
Also, as I pointed out in my comment, there was a bug where clicking on the Meta Stack Overflow (or Meta anything) and then using the keyboard to edit the text field would not change the site that was the migration target. It was very easy to migrate a question to Meta Stack Overflow (for example) instead of Stack Overflow if you clicked on the wrong site and then thought you could edit the text field. Unfortunately, without a suitable question to experiment with, I cannot confirm if this is the case. But I suspect a developer can test this in a pre-production environment with relative ease.