Yeah Tom, I don't consider any of the large holes on flats to be made by anything other than rays. Rays have to get their whole face into digging a hole so leave a fairly distinctive cavity.
Scattered around though are a lot of smaller holes, often with one side having a pronounced sharp edge. I consider these to be made by fin fish of some sort (ie not elasmobranchs). These holes are no bigger than a couple of coffee mugs in size.
What makes these holes is total guesswork though. First you have to find your tailing snapper... then chase it away... then examine the hole it left behind

Goatfish, trevally and porae all make holes. I'm fairly sure snapper do too, but we need firmer evidence.
Great fun studying the sand and trying to figure out what went on on the last high tide though.