Transparency problems when I distort Pdf image size (ie: 100%x99%) then Export. Is there away to fix

I sometimes have transparency problems when I distort PDF image size (i.e.: 100%x99%) then Export. Is there away to fix.   Or at least be able to preflight and know I have an issue.

Mostly I have seen borders and drop shadows that will just go away or other wise not print right but only when I distort the image and only on very complicated large PDF images.  When I print it at same % both horz and vert. this problem goes away.

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