I was bitten by this a number of years ago and complained to the point where they gave me all the miles, but it was annoying. It still is,but simply looking at "Flight Details" will show the stop nature of the flight. I don't like the practice. but it is somewhat easy to find out about it.

I've also had them split a domestic/international into two segments so that I could upgrade the domestic portion with stickers. I also got all the miles for both segments.

One advantage of the current approach is that purely domestic "direct" flights only require stickers for the A->C distance,and not A->B->C.

Cheers.