I'm not sure why the contractor even bothered to call this in this late.Because to him, his problem is EVERYONE'S problem. This is now YOUR problem, the way he sees it, so "too late" is irrelevant.
To me, having a contractor call you "at the last minute" about something is either "passive-aggressive" behavior, or evidence that he has no clue how critical this is. If I were to guess, I'd guess the latter.
The only way you can help "train" the contractor in this case is to hit him where it hurts: in the wallet. This is where you tell him "this is a change order, you know, so it's gonna cost you" or words to that effect. That's the language Contractors understand.