Disputed territorial claims in academic submissions This year I was asked to blind-review a paper which showed a map of China in the disputed Nine-Dash Line borders. I have seen the Nature Editorial from 2011 which discusses and criticizes this phenomenon (and suggests that there is a directive from the Chinese government to show the Nine-Dash line). The map in question showed graphically the values of a certain measured quantity for each of China's provinces. It may be of little surprise that the coloring does not reproduce very well for the tiny disputed islands. But this kind of display does give a reason to show borders. 

Is it appropriate to insert a comment to this effect in a referee report, or can editors be assumed to be well aware of this issue already (or even be annoyed about an unnecessary reminder which may suggest, though not fairly so in many cases, a biased referee)?
Definitely point this out. The whole point of soliciting a review is to identify issues in the paper. You should not assume the editor knows the map on page 7 is inappropriate, just like you shouldn’t assume they are aware that step 5 of the methodology is unsound. The editor may choose to ignore your comment, but that is up to them. They should not be annoyed by a legitimate comment like this.

There is no justification for using scientific articles to advance territorial claims. If a political map is included, it should be clear when borders are disputed -- it's factually inaccurate to only present one claim. And one also questions why a political map is needed in the paper.