White box behind part of pdf in InDesign

I had a pdf that was absolutely fine and then I placed it in an InDesign document and it still looked fine.
On saving from InDesign as a pdf this is what I got...;
Any light to shed on why there is now a white square behind every tree?
Thanks

Hi and thanks Bob for the link but I'd already seen that.
As per the last comment in the thread from 2013...
I still can’t get the extra boxes to disappear when I PDF my indesign file to upload.  My Simulate overprint box won’t even light up to check and try.
Is this a new problem with CS6?
Thanks
Lizzie

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