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How have you created the PDF file?
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This has been observed for a long time with PDFs. What often can help is to change magnification and to zoom in closer. It doesn't necessarily make sense (to me), but zooming in seems to allow more accurate selections.
Keep in mind, though, that PDFs aren't necessarily 'built' the same way that the eye sees them. PDFs are created in many ways from many source applications... and it's a gamble to edit at times.
Good luck,
Dave