Seems to me like it has to do with the direction of the wake up with respect to his direction on knockdown. It's like after you cross him up on the ground the wake up loses its invincibility.
Every time he is crossed up, he gets hit by the clone. Every time he doesn't reverse direction, he breaks the clone.
I know I hit people out of wake ups with Smoke on the regular after crossing them up with a whiffed teleport punch anywhere on screen. (Seems that way, anyway when I recall situations from memory)
See if you can KL Xray him out of the wake up after stepping over him?