Do you find you can't edit a library or folder for some reason even after you already checked there is no checked out files in them?
This is most likely caused by some users are opening Excel file on their computer and you have co-authoring enabled on the library. There is no visiable sign in SharePoint for these locked Excel file.
You can see this behavior with the following test and use the App to find who is locking the files easily.
In an document library, make sure "required check out" is turned off to enable co-authoring. Open an Excel file in client application as user 1. start another session with a different browser as user 2. You will find user 2 can't rename/delete the library and folders which contains the excel file. And there is no easy way for user 2 to find user 1 is locking the Excel file.
Now open the App and you will see it can find the locked Excel file by inputting the library URL.