Steps to reproduce:

1. Activate Frontend Messaging on user profile
2. Create a new Scheduled report
3. Press Test on report while some alerts popup are active

Result:

Sent PDF shows the frontend popup (which are unrelated) on the page
See screenshot

Expected:
PDF does not include overlapping popups. 

Note:

This issue happened with PDF manually generated by the Test button. Not sure if it may happen on PDFs generated by automatic schedule.