Hmmm. Well, the Mary Rose was pretty much the first of her kind in the English navy. A new design needing new tactics and new sailing techniques. Earlier ships mostly didn’t even concentrate on guns, they were just used to carry a bunch of soldiers who would then board enemy ships. Cannon were an afterthought, with just a few scattered around the ship; the main fighting tactics were the same ones that the Romans used against Carthage. The only ships purposefully made with a guns in mind at the time of the Mary Rose were galleys that had a small number of long guns mounted along the length of the ship to fire out the front, rather than a large number of smaller guns mounted broadside.
So even the most experienced crew would be “incompetent” in that there would be nobody who really knew what the ship would do or what to do with it (this was back when shipbuilding and ship handling was determined by trial and error, rather than calculations and engineering). And she was re-designed midway through in such a way as to make her ride a lot lower in the water than anticipated. She was a top-heavy ship that rode low in the water with lots of openings in the side not far above the waterline. All it would take is for the ship to heel over at enough of an angle and there would be problems.
The original story that it was a combination of an inexperienced (not necessarily incompetent) crew making a sudden maneuver in a strong wind does work. There have been tests and models done of it, and the results match the theory and also the eyewitness accounts. There doesn’t need to be any additional factor for such a ship to sink in that manner in that situation. It’s possible that battle damage did contribute, yes, but while all available information supports the accidental capsizing theory, there’s not really any additional evidence to support the new theory that battle damage contributed to it. Nor is there ever likely to be, what with half the ship missing and nothing like video or photos of the event to be found forgotten in some vault.