Hello, 

Thanks for reaching out! It is difficult to say what exactly may be the problem, but we recently received a very similar question, and spotted wing drosophila (SWD) was identified as the issue. 

This insect has an ovipositor that pierces healthy, ripening fruit. Most insects have to wait until the fruit is ripe and soft to pierce their skin. The SWD is able to enter the fruit when it is ripening, making it more difficult to control. The affected fruit will turn brown and often develop a fermented, sour smell. 

To control SWD, cleaning up is the best defense. Clean up any dropped fruit or any that remains on the stem at the end of the harvest season. Do not compost the fruit or bury it. 

Next year, you may consider making your own SWD trap to monitor for the flies. Start monitoring as soon as you see the fruit set. More information is available in the first link below. 

https://extension.umn.edu/yard-and-garden-insects/spotted-wing-drosophila

https://www.mda.state.mn.us/plants-insects/spotted-wing-drosophila

I am sorry about your cherry harvest. I hope next year is better!