This is known as Recurrent Corneal Erosion Syndrome.
This occurs when the new layer of epithelial cells close the scratch but do not put down good roots to fix the new layer onto the surface of the eye. Overnight the surface of the eye dries out to a degree when we are asleep meaning that the eyelids can disturb this new layer on waking re-opening the abrasion or scratch. This re-opening is usually small, so the symptoms subside by lunchtime but then recur the next day.
Recurrent corneal erosions can be managed with a thick lubricating ointment, such as Lacri-lube, instilled at night before sleeping to reduce the risk of the new epithelial cells being disturbed. It may be necessary to use lubricants for three months to allow the new cells to embed fully.