Font problem would be my first guess. The question is, if you choose a different font, or go back to the original one, is it OK?

Since you're on a Mac, also try it as Print and when you get the print dialogue, choose "save as PDF" (bottom left) and see if the resulting PDF document exhibits the same problem.

Hi Megan,

Thanks for posting.

This usually occurs when the characters used for blank or special noteheads (more often blank) displays blank in Finale, but is not actually a blank character. 

The easiest test of this is to compare the PDF to your score in Finale, choose the Note Shape tool from the Special Tools palette (Window > Special Tools Palette), click in the measure where one of these noteheads would be, double-click the handle that appears where the notehead would be, and choose a different character.

In Maestro font (the default) you may want to try slot 127, which I would expect to print to PDF as an actual blank character.

Note: You may wish to save a new version of your file (File > Save As) before trying the steps below since you would be making large changes to your score.

If you find that this is the case, I would recommend taking note of the slot number of the original character you used, and then use the Utilities > Change > Noteheads function to change from the old character (you can specify a selected notehead) to the new character (slot number 127). You can select your whole score with the Selection tool and change the errant noteheads en masse this way.

Hope this helps!