The images in the INDD file that shared are cropped within InDesign. Note that the image border doesn't line up with the container bounds in the screencap below.
in5 recognizes the image has been adjusted in InDesign and therefore re-renders the cropped image.
To fix: crop the images in Photoshop first and then bring them to InDesign in a finished state. in5 will then allow you to export with the source images intact.