Both Botrytis and Alternaria have been found on berries that are rotting down. Botrytis can also spread during mechanical depulping. Because the mechanically depulped seeds are treated soon after depulping, it is unlikely that any fungus will enter the seeds. Seed should be depulped mechanically immediately after picking or, if some green seed is present, within 2 days of picking. If seeds freeze you can expect erratic germination and possibly seed death.
Green seed has an immature embryo.
At the time of seed harvest the embryo length is about 0.5 mm. The embryo develops during stratification to about 2 - 3 mm in length. By the time the seed is ready to germinate the embryo is about 5.0 mm in length and fills much of the seed. Seeds are living things - they can drown if they are in too much water, they can dehydrate and die if there is not enough moisture, they can be invaded by pathogenic fungi and bacteria. To reduce the risk of surface pathogens affecting the seed it should be treated with formaldehyde both before and after stratification.