#2 - Dec. 1, 2014, 8 p.m.
I was pretty confused about the functionality of this myself. Lots of people use the Premade Groups Finder tool to advertise Apexis Crystal groups under the Custom tab, and in a lot of the groups I was getting into people were lamenting that Blizzard had cruelly hotfixed out Apexis Crystals from dropping while in raids. But when I went to look at our internal hotfixes, I didn't see anything relating to a change for how they dropped. Turns out there weren't any changes made, just that the functionality is pretty wonky right now. A combination of a bug in how Apexis Crystals were staying active in areas they shouldn't (leading to some misunderstandings of the system), as well as how some areas are being chosen daily, make it inconsistent and confusing at the moment. We have some fixes in the works that should iron it all out.
The intent is and has been that Apexis Crystals will drop in an "Assault" area if that area is active for the day for either faction; regardless of group size. A random Assault region is chosen every day at daily reset, and for that day that location will drop Apexis Crystals.