Based on what I read about the Vasa, the blame goes to the King of Sweden at the time, who was engaged in a game of oneupsmanship with the King of Denmark. He ordered that the ship be built on a very short timeline which didn't allow an actual proper redesign from a single gun deck to a double gun deck, so it was done on the fly, without actual plans, causing the ship's center of gravity to be incorrect. The ship needed to have a deeper hull in order to be able to sit lower in the water to keep it from being top heavy. The amount of ballast needed to keep the Vasa stable in the water would have brought the 1st level of gun ports below the water line.