You can only let the mate in the shipyard repair your ship if you have:
- 1000 pearls or premium
- 0 HP
- a mate
To repair your ship if you have over 0 HP, click the repair button in the menu in-game:
For this you will need a mate.
If this doesn't solve to problem, you will need to post your user-ID so that a moderator or administrator can look into that for you.