Preview - cropping location issue

Give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE 1: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

NOTE 2: if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode. This makes it act as a wired keyboard as will insure a successful boot into Safe Mode.

To find out if it's system wide or user specific, try this...

Open System Preferences>Users & Groups, unlock the lock, click on the little plus icon, make a new admin account, log out & into the new account.

Does it work in the new account?

we have exactly the same problem here in the office. various pdf files that we want to cut in preview are not cut correctly. the dimensions of the area are correct, but it is always cut at the bottom left and not exactly the area that we have selected (e.g. in the middle of the pdf page)

Are you doing it this way?