try quitting the program you used to launch the pdf (like preview). then try emptying the trash. if it doesn't work, try quitting other programs. and if that still doesn't work, try restarting.
Knowing what's open/attached/mounted. That's what this was; it's not a problem, it's a protective measure. You can't delete things that still have a dependent process active. Best analogy is try to delete a file from a CD. You can't, but the Mac allows you to place files from CD-like images into the trash while the image is still mounted.
You'll get used to it, I still occasionally forget to unmount a dmg before deleting an app launched from it. No biggie.