I know there was some features on the test server which never made it to live, one being archery to damage ships. From what I understand the idea was scraped, but part of the coding for this idea was forgotten about and left in place to make it to live. Specifically you can no longer repair ships while sailing them.
[10:01:33] You cannot repair the boat while it is being commanded.
Some folks like to imp things as they travel around, you should be able to work on your ship as well, could this piece of code be looked into and possibly removed if it was just an oversight?