I've received an aep file and there's the following thing that drives me nuts:
There are obviously two overlapping shapes that where only the exclusion is filled:
Nothing special so far, but there are no masks included and also no Merge Paths:
So there are only two paths included (one for the circle and one for the rotated, overlapping rectangle), so which settings were used here to achieve the exclusion? I personally would have used Merge Paths to achieve this result, but this is obviously not the case here.