Why can't I save pdf files from Safari?
The problem appeared to be that Safari didn't support downloading the PDF from the popup provided by the website (in my case 1Password with its Emergency Kit PDF). Instead I had to use CMD + S or use the File menu in the Menu Bar to save the PDF.

1Password informed me "That is expected behavior — Safari doesn't fully support downloading the PDF from the popup we provide." One is supposed to press command-S or "File > Save As" when I reached out to them.