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Which application do you use to see those boxes?
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adobe illustrator
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Are these after saving as PDF and opening the PDF in Illustrator?
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these after saving as PDF
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And were they saved without Illustrator Editing Capabilities?
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Yes
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That is to expect, Illustrator is not a real PDF editor, it can only open reliably pdfs that were saved from an Illustrator file with Illustrator Editing Capabilities. This one comes from InDesign. You may have more luck by opening it in InDesign (or use the InDesign file for editing).
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Yeah, InDesign does not create edit-friendly PDF files. Technically Adobe Illustrator doesn't do so either; when the option "Preserve Illustrator Editing Capabilities" is checked when saving a PDF out of Illustrator it really appends Illustrator .AI data to the file. Depending on the artwork being saved the setting can make a huge difference in terms of file size. Anyway, PDF files generated by InDesign can be a real mess when opened in Illustrator. It's better to just edit the original .INDD document if possible.
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Or when it was saved from InDesign and you do not have the InDesign file: https://www.adobe.com/learn/indesign/web/convert-pdf-to-indesign-document?learnIn=1
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Issues like bounding boxes around gradients are one of many possible artificafts of importing PDF files into Illustrator. I can't recall ever seeing this problem when exporting native Illustrator artwork as a PDF file.
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