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First, it it your port? :D

Second, if it is, do you control the province?

Third, is it certainly a coastal province?

Fourth, if it's a small island, are you sure that you clicked on it, not missed by 1/10 inch?
 
First, it it your port?
Yes
Second, if it is, do you control the province?
Yes
Third, is it certainly a coastal province?
Very. It is an island and it has a big anchor
Fourth, if it's a small island, are you sure that you clicked on it, not missed by 1/10 inch?
Yes. I howered over and it stood harour. I also clicked everywhere around it.
Something for the X-files?
 
And Viti Levu is the site of a persistent bug in this respect. Don't worry, it affects everybody. Just don't build any ships there.....oh, you already did......oops!
 
There are three areas on the map where ports can appear, but can't be used (this is a bug, by the way). You've found one; the others are on the west coast of Hispaniola and near the southern end of Chile (can't remember the names just now).

BTW, disband your ship in Vita Levu. You'll never be able to get it out, so don't spend the ducats to maintain it.