First, the PaperPile PDF viewer is my favourite online PDF viewer and annotator; easy to use and quite fast. I am having an issue though with text searches within the PDF. In one document I tested, when I open a PDF in Preview on mac, it finds 30 hits for the word I am searching. In the PaperPile PDF viewer it only comes up with two. I tested multiple PDFs with similar results. Anyone else with similar issues? Work arounds?
There are many possibilities why this could be the case. Can you send the PDF and the exact phrase you search to firstname.lastname@example.org so we can have a look?