Hi Becki,
Glad to hear the "-nodisplay" option allows you to get the full image.
There have been a number of issues with Qt on Mac OS X within PyFerret (especially with the Sierra release; a little better in High Sierra and somewhat better in Mojave). I am seeing this issue with PDF saves from displayed plots on my conda installation of PyFerret on Mac OS X Mojave. At this time my only suggestion is to save the journal file and then recreate the desired plot(s) by re-running with the "-nodisplay" option.
Karl