See Topic: Nether icons in the Sitemap are set to default and can't be set.

3.1-beta5
paper 1.16.4 build 265

Edit: Same for the favicon (dynmap.ico) as you see in the screenshot above, normally it's that:

Not sure if this is still relevant as it is a very old issue:

Was not able to replicate this issue:

Make sure you run /dynmap pause all before making changes to the map icons.