I heard that a banca boat dragged across a reef causing some minor damage to that local area. Of course the locals wanted to fine the guy (bribe me or else). But I dove Apo twice this year and it was beautiful as usual, I did not notice reef damage. I think right at the main anchor area for the main settlement, there must be a lot of anchor damage and possibly boats dragging. Nobody dives there anyway. It's a small island on the map, but has a lot of good sites when you are there, really a nice area.
One thing that annoys me is a camera fee. What's with that? Because they can get it, they charge P300 to use a camera, in addition to sanctuary fees. Well, it supports the locals, who presumably fish less. Although I saw a lot of fishing when I was there.