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If they're are black spots and not holes, it is likely a fungus. Treat the plant with a fungicide.

As long as you allowed the herb to throughly dry, it is perfectly fine to rinse it off. In fact, most people do. It is not uncoomn for them to lose some of their color after harvesting or wilting. For more information on harvesting and storing herbs, these articles should help: https://www.gardeningknowhow.com/edible/herbs/oregano/learn-how-to-grow-oregano.htm
https://www.gardeningknowhow.com/edible/herbs/hgen/how-to-dry-herbs-various-methods.htm
https://www.gardeningknowhow.com/edible/herbs/hgen/freezing-herbs.htm

This article should help: https://www.gardeningknowhow.com/edible/herbs/hgen/how-to-dry-herbs-various-methods.htm

If they are in pots, the oregano and sage can make it through the winter in the garage if you remember to water them about once a month. They will look like they are dead, but they will just be dormant. The basil is just best to plant new from seed next year.

All leaf spot diseases can be controlled by decreasing or eliminating overhead irrigation, minimizing leaf wetness periods, discarding heavily infested plants, and applying preventive fungicide applications. The same type of fungicide can be used on all of them. Also, removing and discarding diseased leaves will greatly reduce the infection and should provide sufficient disease control.

This article should be of some help: https://www.gardeningknowhow.com/edible/herbs/oregano/oregano-problems.htm