I had this problem. Some experimenting helped me solve it.

1. It's now a lvl3 building.

2. Try building buildings closer to the beach, it seems you need to be closer to the beach now.

I don't even have the "Harbor" available on my buildings list, to even try to construct! Will it not even appear on the list until an available beach tile exists in range of the level 3 city? I've triple-checked, and the tech is on my "completed" list. But it's like I haven't even researched it.

We honestly need a detailed FAQ for building a harbor. Too many people have trouble building them (myself as well, this patch around, apparently). Things like exact tile/influence distances, etc.

Why would you want to build it? It is so limiting and only in the rarest of occasions does it ever benefit. I have been playing since August and it is the lowest of priorities on my tech list. I am curious as to what advantages it gives you. Would you mind sharing?

Yes. And given that this is a game, it might have simply been for fun.

 Also a very few random maps have islands in them, the ones I've found so far all had wicked resources, but I've only seen that 1 in about 15 games or so. No clue if thats the average for it, or still included in 1.1.

Slay food! Eat Enemy!

We seriously need a cannibal side that heals themselves by eating the troops/pop of other sides, but everyone declares war on sight on them.

I built a ship to explore the coast but it has little benefit at this point