Please make sure dock more ships in your Ship Dock so that you have less than 40 ships in your waters. Once you have less than 40 ships, you will be able to undock back into your Cove.
Also, please note that the game currently counts any ships you have stored in your Aerial dock as well. If you have 2- 4 ships stored in there, they will count as being in your Cove and you must have less than 36- 38 ships in your waters in order to undock more ships.
We have adjusted the amount of ships players can have in the waters of their Paradise Cove based off of what device you are using. If you are using a lower-end device such as an iPhone 4 or iPad 2, you will most likely only be able to have 10 or 25 ships undocked to help reduce crashing in the game.