DIAGNOSIS The scanner driver is not set to use the ADF as the source. It's defaulting to the flatbed.
FIX In the Canon IJ Scan Utility on your computer, click Settings. Change the "Document Source" from "Platen" to "Auto Document Feeder". Save the setting. Place your document in the ADF tray and press scan on the computer.
IF THAT DIDN'T WORK The ADF rollers might be dirty, causing a misfeed that the sensor doesn't register. Clean the rubber rollers inside the ADF with a damp cloth.
HEADS UP The ADF has a maximum paper weight. Using thick cardstock can jam it and strain the feeder motor.