I made an account to say this exactly and wanted to report this glitch. When ending Act 1 (boarding the ship with Malady) the character wearing the Captain's armor set as well as the gloves from the Devourer's set had his pants unequipped. It then appeared as an unidentified leggings in his inventory but could not be identified using Loremaster skill or any vendors who have Identify capabilities. After saving and trying to reload the game crashed.
I tried reloading to a save before the act transition and got rid of the unidentified leggings and bought new pants from Exter on the ship. I proceeded with the storyline but after the fight against Dallis on the ship and reappearing on the ship after the Hail of Echoes, I set sail for Act 2 and found that once again the pants were unequipped and now unidentified, and the second player character also had an unidentified helmet and necklace that I don't know I actually had in my inventory now. That character was not wearing any of the gift bag armor set pieces.
I reloaded to an auto save of the same playthrough in the Hall of Echoes, before the transition to Act 2, and unequipped all the Gift Bag armor set items (Captain's hat, chest, and feet plus the Devourer gloves) as well as the leggings. I tried to transition to Act 2 with everything unequipped and didn't seem to have any duplicate items this time, though I have not done any testing after that.
I doubt this is a glitch because it seems like the save is sometimes corrupted. I am hoping that this does not result in lost saves and having to play Act 1 again. Hoping that someone at Larian can see this bug post and look into it! I was really excited to see even more gift bag content and love playing this game in so many different ways!
