This is a strange issue, and really your web hosting company may have to investigate.
You may find that your web server sometimes redirects requests for the PDF file to your home page. If you enter the PDF URL directly into the Edge URL bar you will probably see that it sends you to the homepage...
So instead of sending the PDF to the viewer, it sends the home page of your site instead... of course that causes problems!
So this is not normally an issue with the PDF Embedder plugin per se - it (correctly) detects that the 'PDF' downloaded isn't really a PDF.
Hopefully your web hosting company will be able to help here. One other customer ran into this problem and their hosting company found that their 'hotlink protection' was causing this problem, and everything was fixed once that was disabled through cPanel. In fact, you may only need to check the option in cPanel to allow direct access via a URL entered directly into the browser.
Once the PDF is served correctly by your site, the plugin should have no problems at all.
Please just send us a link to the problem page on your site if this doesn't help you.