Upvote:6
The only solution seems to be contacting the consulate directly and asking them what they can do. Since it's a mistake, they should be able to correct it easily but if they won't, there is no established procedure to get an extension quickly. A trip to the consulate will however be needed in any case. Incidentally, it's a bit stingy of them to do this as issuing longer visas is recommended for seafarers, given the nature of their work.
If that does not work, you could still try to get a visa when arriving in port at the end of your contract, seafarers are specifically mentioned in the relevant regulation (article 36 of the Schengen visa code) and associated Handbook as one of the very few categories of people who can apply for a visa at the border. I have no idea how it works in practice or if it could be a problem for your employer but it is at least legally possible.
You will probably need your seaman's book, a cover letter from the company that hired you and the details of the ship (as you presumably did for your application).