I've got the boat glitch too.
Done 2 side missions for the Haitians. When I talk to Emmanuel, game says I'm done and one of my objectives is to get more rackets. After a while, I get the boat icon again, exactly in the same place I had already cleared out. I go there and there are no enemies and no boat. I reload the game and sometimes the boat sign spawns on the ground, and other times in different locations. My objective changes from "get more rackets" to the same objective "steal the boat"I had already completed before.
I'm loving the game, but this is fucking annoying. I've already reloaded a previous save file twice and got the same problem every time. Now, I'm going on with the main missions and I'll avoid finishing that side quest until it's fixed, which hopefully is soon, since many people are having exactly the same problem.