Read up on something called a
piddock.
Do these holes look like what you have?
I've never heard of a tropical piddock as I have only seen them in temperate areas, but hey, stranger things have happened. I think this is your culprit.
Depending where your rock if from I'm going to guess that it's a
Pholas orientalis or
Petricolaria pholadiformis, but then again it could be any bivalve with an "angel wing" shell