I don't have a way to reproduce the overlap bug at 100%, but in case it helps, I believe every time it happened to me:
was during the phase where my opponent had to declare his blocking units, against my attacking units.
I was moving (a lot) my cursor over the oracle's eye (hovering/not hovering), while the opponents was moving his units.
Eg:
I'm attacking with 2 units AU1, AU2. Opponent has 2 units DU1, DU2.
He moves DU1 in front of AU1. Then moves DU1 in front of AU2. Then puts DU2 in front of AU1. While he does all of this, I'm flipping a lot between the oracle's eye view and the current board view. And sometimes, DU1 and DU2 would overlap in front of AU1.
Like if the generation of the oracle's eye view was conflicting with the events of the opponents moving units on the board. I believe I encountered a few crashes in those situations (not full client crash, but match crash, forcing the client to reconn...