The weight hole is always the one in question on this. He can throw a ball that has a thumb hole without putting his thumb in it as long as that thumb hole could be used if he chose to; however, it can't also have a weight hole. So, if, as you say, his ball had four holes (assuming you meant two finger, one thumb, one weight hole) then, yes, that was illegal.
As a previous poster asked, did you tell him that he was in violation at the time? I don't think that you're required to, but I think that would be the best starting point. Now, if he's been told before about this and is choosing to ignore it, then that's a different story.