It could be. "Duplicate Folders" are classed as duplicates according to the input criteria you give the program.
Reasons that two folders classed as duplicates may have differing numbers of files:
You have an exclusion filter such as size or date range, or file type.
A folder contains files (or subfolders) with the system flag set, and you have the 'Protect important system folders' option turned on
These situations means that files are ignored, and not taken into account when classifying the folders. If you click on the folder in the duplicate folder list it will show a list of files to the left. Any files shown in GREY are outside the scope of the duplicate scan and have been ignored. This may account for your discrepancy.
Note that the program will not remove these extra files, even if you mark the folder. It deletes by file, not folder, so will only remove duplicates that are listed in the Duplicate file list.