I might be saying the exact same thing as DFlynSqrl but I’m not sure so I’ll give you me explanation.
Phase Explanation
C First player assault phase
D Second player assault phase
E Casualty phase
NEXT TURN
H First player assault phase
I Second player assault phase
J Casualty phase
So, if the sniper uses HeadShot on either phase C or D and succeeds, you place a face up disrupted counter which will not be removed in phase E, but in phase J. If your vehicle gets attacked later in the same phase (C or D), then its defense is lowered by 1 and if the HeadShot was made during phase C, then your vehicle as -1 penalty to its attack in phase D. If your vehicle receives 1 hit during the same phase it got HeadShot, then you place a face down disrupted counter. After phase E, you manage the “HeadShot counter” the same way you would manage any other counter. (Of course, if you end a casualty phase with 2 face up disrupted counters, you can remove the second one for it doesn’t change anything)