This can mean a couple of things but the most likely causes are either that the PDF is open in another program such as Adobe or Preview or that some files are in "read only" mode, meaning that they cannot be renamed, which file management does.
In order to find out which PDFs are causing the trouble, click on the "see more" alert within the file management settings which will appear following the appearance of that message.
This will show you where on your computer you can find any PDFs which are unable to be moved and check to be sure that they aren't open else where and are in "read & write" format. Also, be sure to check that the folder they are in isn't in "read only" format.
Be aware that in order to change the privileges of a file, you must be using an account on your computer with sufficient privilege access - such as an admin account. Typically, guest accounts or accounts issued to you by your place of work or by a campus will not have these rights.
If you have any questions, please don't hesitate to contact us at ReadCube Support