Cards can fail to be scanned for a number of reasons including being heavily damaged or altered, an issue with our image recognition software, or it may not have been a Magic card at all (we are planning to add support for other card games soon though!).
Cards that fail to scan are placed in the lefthand stack whether you are just scanning or sorting too.
If you're scanning, at the end of a session the entire lefthand stack will be cards that failed to scan. It is often worth reloading this stack into the center stack as cards can be recognised after a second scan. If there are cards that consistently fail to scan, it is usually best to process them manually - either scan them with the app or add them manually on the Build page.
If you're sorting as well, at the end of a session the cards in the lefthand stack will be a mixture of cards that failed to scan and cards that didn't match your sorting criteria. If the cards that don't match your criteria are going to be reloaded and processed again, it's likely that the cards that failed to scan will be handled correctly on the second run so load the whole stack.
We are working on systems to help process cards that fail to scan including the ability to view the image of card and confirm recognition and failed scan alerts.