I try not to automate workboats anymore, I have no clue how the AI decides to work things. I had a resource right outside a city, and simply hit automate, and checked back later, and it appears the AI thought it more important to work a tile that no city has access to, on a resource that I already had 2 of. I have also had a workboat park on a resource (might be clam) and never work it. And I have seen the AI do the same for computer players. Just park it on top of a resource.