That is why you use search and replace. Find the bad part, put in the find search area and in the replace part put nothing, then replace all, making sure it is set for all HTML files.
It should look something like this in code view:
....last few words of paragraph.</p>
<p>This is the start of a new paragraph. And it continues on.....
Anything else will add the extra line and should be deleted using search and replace.