Have you verified that your world map isn't actually wrong? There are issues with Minecraft itself that can cause chunks saved to move around or even chunks from previous worlds with the same name (Minecraft saves world data for worlds with the same name to the same folder, and sometimes these chunks from other worlds don't get deleted) to be used.
I have setup dynmap to render my SMP server. As listed below you will se that something is wrong. There is water where there should be land.
https://gyazo.com/a0019a8e561e365d2f99fb225eb1c405
What version of MC is your server running and what version of Dynmap is producing the map shown?
[Not familiar with Dynmap, but that picture looks like version incompatability to me…]
I play on 1.13.2 and use dynmap 3.0
Dynmap 3.0 beta-3 seems to be correct for Spigot/Buckkit 1.8.8-1.13.2 & various versions of Forge through 1.12.2 see https://forums.dynmap.us/viewtopic.php?f=5&t=2
This looks like the Dynmap support site https://forums.dynmap.us/ and shows enough activity that it may be a better source of help…
Have you verified that your world map isn't actually wrong? There are issues with Minecraft itself that can cause chunks saved to move around or even chunks from previous worlds with the same name (Minecraft saves world data for worlds with the same name to the same folder, and sometimes these chunks from other worlds don't get deleted) to be used.
Is there a fix for this?
I do have that version. I will try it.