Thank you for the post.
To attempt to replicate this issue, a new database file was created in FileMaker Pro 12.0v3 installed on a Mac OS X workstation:
1. A single field and a single record of information was added.
2. Entered Preview Mode and selected the icon "save file as PDF."
The PDF was created successfully and saved to the desktop. FileMaker Pro 12 continued running without issue.
Do I need anything else in order to duplicate?
I recommend running a recover on these files to see if damage is detected. Even if no problems are found by recovery, then I'd test the recovered copy for the same strange behavior.
Things to keep in mind about Recover:
While Recover almost always detects and fully corrects any problems with your file...
1. The recovered copy may behave differently even if recover reports "no problems found".
2. Recover does not detect all problems
3. Recover doesn't always fix all problems correctly
4. Best Practice is to never put a recovered copy back into regular use or development. Instead, replace the damaged file with an undamaged back-up copy if this is at all possible. You may have to save a clone of the back up copy and import all data from your recovered copy to get a working copy with the most up to date information possible.
And here's a knowledge base article that you may find useful: What to do when your file is corrupt (KB5421).
If recovery shows no errors, then can you create a new simple test file in FileMaker Pro 12 that replicates this particular behavior?