I have experienced this on the Windows version - I LOVE the features of the new built in PDF annotator.... however when moving from the PDF in tab, back to the library tab, and back again, the PDF itself had rotated through 90 degrees and is now opening sideways at all times within Zotero, but not through Adobe Reader (using the file in the Zotero library). Perhaps simply implementing a "rotate 90 degrees" button that one can press until corrected would be enough of a fix if this occurs?

I found the rotate option in the Edit menu rather than the View menu.

Zotero fan here. I just spent quite some time trying to figure out how to rotate a page with a table to landscape, just to view the table. I found the answer in this forum. It's great that this functionality exists but I never thought of checking the Edit menu. I started by checking the View menu, then I tried right-clicking on the pdf (I'm on Windows) and checked the context menu. I tried poking around the screen for a rotate icon. Then I did an internet search and found instructions for the R and Shift-R hotkeys, which didn't work, which caused me to double-check that my Zotero version is up to date, even though I know I have auto-update on.
Finally I found instructions about using the thumbnail view of the navigation pane, which I then had to go and find since I had previously never used the pane.
I love all the new changes. The simplicity of turning annotations into notes is a total game-changer. Thanks for all that you do. If there was a spare moment, maybe a right-click context-menu option for view rotation, or the return of 'R' or 'Shift R', might be considered?