The Tubbataha area must be pretty badly charted as it seems many ships are running into reefs often. The lastest is a Chinese ship carry endangered Pangolins. Just 2 months back, a US warship ran agroundon a reef as well and caused much damage to the reefs. Even Greenpeace's Rainbow Warrior ran aground there. This is on top of the various liveaboards which have also hit reefs in the past!
But like this interview suggests, it's best to ask the locals and use the same GPS system they use!