I assume that "Frigate" your talking about is a class 4 ship usually used in port controller lost ship quest, governor quest and stolen bride/groom one. Believe me that ship is one of the bugged ships in the whole mod. You literally CAN'T DAMAGE the ship, not the hull, not the crew, not the sails while they totally CAN DAMAGE yours. Funny thing is once you got the ship, it's no longer invulnerable. Though it takes little to less damage than other ships do, it's still a bugged ship.
The Light galleon class 6 is also one of them. Knowing the problem, i managed to take one for myseft, store my HMS Victory in the port then fully upgraded the galleon. Guess what! The ship is beyond god like, though it only has 20 guns and less than 7000 Hp, no ships or forts can birng my ship to the bottom of the sea even when shot with a full board to board by the quest FD
Back to the topic, if you want the ship that bad then you can use debug mod. To activate it go to your game folder Program/_mod_on_off.h, search for the line #define MOD_BETTATESTMODE then change "OFF" to "ON". Load your game, in game hit F11, look to the bottom right of the screen for "Installtion". Hit it then check the line "BetaTestMode" or something then hit the X on the top right to exit (If you press OK then you'll be teleported to COAS and f*** up your game). There you go! Now you can check on the shipyard for any ship available in the game. I recommend you should create to 2 save files, 1 b4 activating betatestmode and 1 after as it's quite dangerous if not used correctly and might affect your game A LOT.
PS: For more information 'bout bugged ships, see here http://forum.piratesahoy.net/index.php/topic/17950-crash-repeated-almost-constant-for-the-screen-in-the-sea/page__st__40. Posted by Joe Dagger