(I deleted your comments in the other threads, since you're conflating multiple things here and it wasn't clear what you were referring to, and because posting the same thing to multiple threads is distracting and unhelpful.)

These are two separate features:

1) Clicking to jump to a reference is a standard feature of PDFs that exists in all PDF readers — the links are in the PDFs themselves. There's no way to disable that. (Also, I'm not clear why this is a problem? If you don't want to follow a link…don't click it.)

2) The popup window that shows linked and cited references and figures is a Zotero feature. It can't currently be disabled.

I apologize for posting the comments multiple times. I thought it would increase visibility and the chances of getting helpful advice. I won’t do it again in the future. @dstillman

I have the same problem with the pop-ups when reading/highlighting. Has anyone found a work around?

The problem that the OP describes with the unwanted pop-ups.
The pop-ups get in the way when I highlight a paper (PDF) using the desktop version. Although the pop-ups are a cute feature, they can get distracting if you actually read and highlight the paper from a computer screen.

I find that these pop-ups can be quite distracting when they appear above the portion of text I'm currently focused on. The unwanted pop-up ends up blocking the very words I'm trying to read at that moment, which impairs my ability to smoothly read through the passage.
I know the intention may have been to provide the pop-up when the user holds over the link to select it. However, this distraction can also happen simply when moving the mouse pointer to a new spot to begin highlighting. During the natural flow of reading and highlighting, some readers often move their mouse over the text, selecting passages as they go. So even without clicking and holding, the pop-ups can disrupt the reading experience.
While some users might have a different experience, there are journals out there that are minefields of links, making this issue particularly problematic.

I also would like to be able to turn off this feature.

It does not work properly on

1) equation heavy articles.

https://s3.amazonaws.com/zotero.org/images/forums/u8123077/h3r8wpujqhu80wfyhurq.png

2) review articles with already existing refs.

https://s3.amazonaws.com/zotero.org/images/forums/u8123077/uxvcdm09p46xdui5hi4h.png


Edit: I would like to add/stress that this is an extremely useful feature of zotero, however, when it does not work on a pdf that the user spends a lot of time and not being able to use already working hyperrefs, it becomes frustrating.