I had suspected that there was a bug in power management on some (at least) models of Mac for some time. I leave my iMac running all the time, and have set it to sleep the display and system, but not to sleep the hard drives. When this was set using the Energy Saver pane, I was surprised that whenever I woke it up, I could hear the internal hard drive spin up.
However, as I have recorded elsewhere, El Capitan has more general problems in Energy Saver, which differs substantially between models. On this iMac Retina 5K 27″ Late 2015 (running OS X 10.11.3), the Energy Saver pane differs from other models in inexplicable ways. Most importantly, it does not separate display from main system sleep. It is possible that this is because this particular model cannot separate them, because of design limitations or a bug in its power management.
To assess this further, I have produced custom power management settings which require a display sleep time of 30 min, main system sleep of 120 min, and hard disk sleep of 0, which equates to never. These were produced by MacPilot, and confirmed by inspection.
When operating under those settings, display and main system sleep function correctly. However, when the main system goes to sleep, the internal hard drive within the iMac’s Fusion Drive is spun down at the same time.
This is reflected in DriveDx’s Power Cycles Count for the hard drive within my iMac’s Fusion Drive, which is currently 766, and is incremented by 1 every time that I wake it from system sleep.
So if your Mac is affected by this and you want to prevent the disk(s) from being spun down, the only option is to set system sleep to Never. It does not appear possible to have the system sleep but not the drives. I do not know how specific this is to certain models (I suspect that many are not affected), nor whether this is confined to OS X 10.11.3.