Something to try.
Open the PDF and go to the page of interest.
Open the Tags panel.
From the Options menu select "Find".
In the Find Element dialog do a Search Page for each of the choices on the drop-down menu for "Find".
This may yield some pertinent information.
As CT Dave stated, Find should allow you to find and tag these, then they could be converted to artifacts. If you can select them with the Edit Object tool (Content Panel, Acrobat 10; or Touch Up Object Tool in Acrobat 9) you could right click on them and convert to Artifact in the main display window. This would eliminate the need to tag them to get rid of them.
Tagging them may reveal what these mysterious boxes are. Can you select them with the Edit Object Tool and try deleting them to see what, if any, content is lost?
I wonder if this document was created in Microsoft Word and if so, is there is anything going on in the Header or footer? Like a string of paragraph returns or a drawn vertical line or ?? Even so, Header info usually tags as background artifact, but of course that depends on how the PDF was made, what version of Word and Acrobat you are running, the OS and other factors beyond our control.
I'm very interested to know what you find out.
You can also whip through your tags hierarchy and look for empty tags (if it's a small-ish document). If you click on and open up a tag/folder and there's an empty box there simply right-click on the tag and delete it.
As was mentioned the touch up tool is a great help. You can fit your doc to window (zoom level) and then go through each page and do a select all. See if any empty boxes get highlighted in blue. You can delete these objects.
As raeben3 said, there are weird interpretations of para returns and other crap-ola especially from Word. You can delete them of make them background elements or artifacts. If you work in InDesign just Google "accesible documents in InDesign" or something similar. Adobe has an entry-level guide that helps yous set up accesibility features in InDesign that persist as the document moves forward with rounds of edits. Saves work.