This was a a known problem in Mountain lion onward where the OS ignores HDD or download activity and simply sleeps in the middle of a long CPU intensive task or download. I still experience it on my Yosemite laptop and I have to use Caffeine to stop it. If I forget to activate this, the download stalls. Any idea if there is a more robust or automatic solution? I'm holding off upgrading my main production machine to Yosemite mainly because of this bug. I've left Apple feedback but I find it completely ridiculous that something so simple has been ignored for so long or simply won't be addressed at all.
