The flag dialog is under the left sidebar text. This only started happening over the past day or two.
Using Safari 12.1.1 on MacOS High Sierra.
Successfully reproduced on StackOverflow and PPCG, along with their respective metas.
This is building now.
There was a change to z-index in Stacks which bumped the leftnav up to 5000. The thing is, though, leftnav didn't need a z-index. When it's inline with the page, it can just have its natural z-index, and when it's living in the top nav, it gets the standard z-index for a top nav dialog. This was probably left-over from a previous implementation.