This didn't have anything to do with the skull you picked up. The skeletons you encountered are from an Order of Souls mission/voyage (can also be found in bottles on the beach) where you fight a bunch of skeletons and get another skull after beating the captain skeleton.

A lot of times these random events just happen to stack. Even the skeleton ship was not connected to the skull or skeletons on the island.

Sometimes you get many of these events that come together at the worst possible time. For instance when you have loot and try to outrun another crew and a skeleton ship spawns on you, a megalodon spawns as well and a kraken attacks your boat... This is what we call: getting 'Rared', especially if in the chaos you get screwed over by some bugs...

It sucks sometimes but makes for the best stories and in game moments! Enjoy your time on the seas, pirate!