Hello and thank you for this post.
It is hard to say without looking into the PDF document in question closely.
It sounds like on whatever software the file was produced did not put text blocks, but instead has added text as comments.
In Expert PDF you may Hide Comments with the button under Review module.
If these comments contain no information, please try to purge these mark-up annotations by selecting each one and delete it with the key button on keyboard. Save the PDF document after clearing up.