Steps to cause this problem:
- Open a page that contains refs.
- Select a ref (click on a "") and copy it (Command-C).
- Click the Cite button and choose the "Basic" form.
- Paste the ref into the dialog.
- See the black cloud!
- Save the page.
- File this bug.
This happened in Safari 9 on Mac 10.10.5. I have not been able to reproduce this again.