I use an e-book reader (Icarus Excel) to make notes on PDF files. When looking at the output PDF (which merges the notes with the PDF document) in Adobe Reader, the notes are present. However, the same document, when opened in Preview, does not display the notes. What would be the reason behind different ways of displaying the same document in the two programs and how to make Preview "see" the notes?
Preview.app is a mediocre PDF viewer at best. There is not much you can do, except to complain to Apple to finally get Preview.app up to date.
It is possible that the eBook reader you are using is also not quite up to date, and it writes slightly defective PDFs which Adobe Reader is able to fix, but Preview.app isn't.