Hi Carla, 

This is SWD or spotted wing drosophila. Unfortunately, these larvae damage the fruit and cause this bruising. Eating them won't necessarily harm you, but we do try to avoid it!

I would recommend doing a float test on any cherries you suspect may have SWD or bruising. Here's a procedure: A Detailed Guide for Testing Fruit for the Presence of Spotted Wing Drosophila (SWD) Larvae (oregonstate.edu). Basically, floating them in sugar or salt water allows forces the larvae out of the fruit and makes them easier to identify. The bruising is most likely caused by SWD larvae, whether or not you can find them! 

This was a tough year for SWD in cherry production. Going forward, keep in mind that they really prefer soft, more ripe fruit. If you can harvest fruit on the earlier side, you will have better luck avoiding them.

Best,