The ship equipment vendor has a list of your ships at the top of it. This is so that you can change your equipped ship without leaving this screen.
If you have one of your own ships selected it says "You already own this item", so that you wont think that your own ship is for sale. If you click on a piece of equipment like an anchor or a set of sails that message should go away.
If this doesn't help, please specify the name of the vendor and the name of the item you are trying to buy so that we can better help you.
Some additional details would be helpful. What ship/ships do you own? Which ship do you have equipped? What equipment are you trying to buy, and from which vendor? What is your current nautical level? (Lots of ship equipment requires a minimum character level or nautical level to equip it.) Do you have enough gold (or crowns, for crown shop parts) for the parts you're trying to buy?
I am also having this issue with my swashbuckler, in Scrimshaw. Even stuff I don't have, like hull armor, I can't buy because "you already own this item". I've tried it with the ship equipped and without a ship equipped, and can't see that it makes a blind bit of difference. I can't buy. Apparently Ned Scott doesn't need my business. Neither does Juan de la Cosa in Puerto Mico. I have completely exited the game and logged back in to no avail. It's frustrating. There is no way on this green Earth I'm about to try to purchase a better ship, if the chances of me being able to equip it properly are slim to none.
Check your backpack. Mine was full, so it wouldn't let me buy the equipment, but once I sold some stuff off, it did let me purchase. Of course, I only found that out when I decided to bite the bullet and try the crown shop for equipment. That's when I got the backpack full message.
It'd be nice if the message at the vendors said "your backpack is full" rather than claiming you already have this item.