Evince highlights wrong regions in PDF
Solution 1:
According to the following bug report, the problem is related to how Poppler handles cropboxes. They say it is fixed in Poppler 0.86.0 onwards.
However, if you are still facing this problem (as it was my case) you can modify the PDF so that it does not have cropboxes. I have been able to do this by calling pdfjam without any arguments:
pdfjam original_file.pdf -o fixed_file.pdf
I am sure there must be better ways to do it, but I have only found this.
I have tested this method with this pdf and it works.