While I cannot reproduce this on demand, I can pretty reliably...maybe 1 out of every 15-20 gathers if i try, I've been able to reproduce this about 5 diff times last night while trying. (At work, so I don't have any screenshots) As someone mentioned, I believe it to be an issue with collision. I'm fortuante to be a server admin, so after my first gathering death and realizing it to not be an isolated issue, I began taking coord readings before gathering, then trying to get myself to die, and teleport back to the location. In virtually every case, when I returned to my backpack, its location on the ground was always in very close proximity to the pile. It is like the models go from a square to a diamond when they reduce in size. I am terrible at art, but here is my best explanation in drawing form...
Observational factors:
Proximity to pile
Resource type (seemed to happen considerably more often with wood)
Surrounding terrain - gathering while at a lower elevation than the resource seemed to cause the bug more often
(apparently) Unrelated factors:
Gathering item - had this happen to me with rock, stone hatchet and pick axe
Clothing - had happen while wearing multiple outfit combos
Crouching/Standing - happened to me equally
Server mods: I run Oxide - bug occured whether Oxide was running or not.
I'll post my system specs if needed, hope this helps!