Editor iD is not the right editor for this job.
This editor can't handle multipolygones. 
Your intention was okay ofcourse. 
You need a lot of skills to do that.
Now the problem here was that two outers of the same multipolygon are connected with eachother.
Thats will give problems. 
So please leave the mapping of harbours and coastline to the openseamappers or contact one of these mappers.
https://wiki.openstreetmap.org/wiki/OpenSeaMap
You may also put a remark on the map with the question that a skilled openseamapper will have a look to the harbour. 

Greetz,
eggie
