First, are you running the latest Face Crop release, version 4.0.8?
When you ran it, it created a data file in the source folder called CropData.txt. Please open that file in Excel or another spreadsheet. The file is comma delimited. So when opening it, tell excel to use a comma delimiter so it separates the cells correctly.
It will contain the crop data for all images in the batch. There will be an “error” column. In that column, does it show any errors for any of the images?
My initial thought was that maybe some images were cropped tighter in camera than what the Face Crop preset was set to crop at. When that happens, it will have to crop those images tighter (unless you changes the empty space settings) to avoid having empty space. When that happens, it will make an entry in the Crop Data file under the error column.
Please let me know after checking the file.