I found a strange behavior associated with the Annotations function. The first screen shot shows a PDF with highlighted text, everything is as expected.
After clicking on the highlighted text in the Inspector -> Document -> Annotations window, all links in the PDF are crossed out (screen shot 2).
I have observed this with several other PDFs.
This PDF is attached in case you want to reproduce the problem.Pichot2016.pdf (3.5 MB)
Thanks for looking into this.
This is related to the structure of the PDF, which defines the content that is greyed-out in your second screenshot as “annotations.”
Expanding one of these “Annotations” elements reveals a long list of items designated “Link.” The way this PDF is organized, the parenthetical matter (citations and descriptive/ancillary commentary) are “annotation” elements, so when you select a given “annotation” in DT3, the document viewer is not only bringing your highlight into focus but also revealing all other “annotations” on the page.
Here is the way the page is organized with each item in the prior screenshot being represented by one of the boxed areas on the page:
I do not know of a simple solution for this but I wonder whether you can “flatten” the PDF prior to applying your own annotations. The idea would be to remove the organizational structure from the PDF so that DT3 doesn’t treat your annotations and the structural annotations the same way. Cumbersome, to be sure.
There is nothing wrong with the file. The items are not “crossed out”. They stripes show Link where they occur in the PDF.
Thank you very much for explaining!
And sorry for being persistent: The easiest way of avoiding this problem is opening the PDF in Preview.
After opening in Preview and selecting View -> Highlights and Notes you may click on the highlighted text in the Sidebar and Preview will bring you to the highlight in your PDF. It will not mark any links (see screen shot). At least in my mind, this is the expected behavior.
I would be happy to see this behavior in DT3 as well, without marking the links.
By the way, the gray stripes obscure the PDF and make it more difficult to read. If you want to show the links, they should be highlighted and still readable.
Development would have to assess not showing the links when selecting an annotation in the Annotations & Reminders Inspector.
Oh this has been like this for years, sometimes it happens to me too. It might have to do with the document itself, who knows!
After selecting an annotation in the inspector the PDF mode is switched to annotation selection (see e.g. Editing bar or menu Tools > Mode) and the annotation is also selected in the PDF view, e.g. to delete or move or edit it by double-clicking. However, in this mode all link annotations are marked using gray stripes, otherwise it would be difficult to recognize & select them 
