A guess: The circles are actually pieces of text. The font is included to the PDF, and it's available for the PDF reader, but Illustrator refuses to read it because Adobe doesn't help uncontrolled font distributing. You would have a theoretical possibility to write something without paying for a font.
Try to open the PDF in Inkscape. Import can work because Inkscape isn't font seller. The unfortunate thing in Inkscape's PDF imports is unpredictable deep multilevel groupings. You may need to apply Ungroup several times or to apply extension Deep Ungroup.
Maybe you can insert a link to the PDF to stop guesses and to get some reasoned help. Use a cloud which doesn't need login.
ADD after the link was made available: The guess was right, the dots are pieces of writing.
I released in Illustrator the clipping mask, selected one of the dots, then selected all of them by applying Select > Same > Appearance. Applying Type > Font > Arial restored the circles. In the next image only a part of the texts is changed to Arial:
When editing PDFs in Illustrator you may need to release and delete numerous clipping masks before you can select the wanted objects. This case needed only 2.
How do I know Arial is the right choice? I don't. It was only a guess. Illustrator tells when you open a PDF what's missing and Acrobat can give also a list of needed fonts. The original is the original. I tried also Windings as a substitute. It seemed to work, too.
In this case Illustrator said
The font AdobePiStd is missing. Affected text will be displayed using a substitute font.
Tried also Inkscape 1.0. It imported the PDF. Import mode "Internal" worked, Poppler-Cairo import didn't.