If you select multiple folders containing files, the bates numbers will be assigned in alphanumeric order to all the files in those folders, regardless of the folder hierarchy (as if the folders did not exist).
If you want to assign bates numbers to specific files first, you should place those documents into a folder and then assign the bates numbers to the documents in that folder.
You can remove any bates numbers assigned in DocReviewPad by pressing Select, select the document(s) or folder(s), tap on Edit > Assign / Edit Bates Numbers > Remove Numbering.