When flagging an answer that is grayed-out because it has a score of -3 or lower, the flag dialog is also grayed-out. If you drag it over a non-grayed-out answer, it appears semi-transparent. The same is true when you flag a comment on a grayed-out answer.
This looks like a regression of The flag pop up on heavily downvoted answers has grey textThe flag pop up on heavily downvoted answers has grey text, perhaps due to this recent bugfix.