Been a long time since I used Cubase but maybe you accidentally created shared copies, so they are treated as one and not real copies?

Shared copies are useful, if you want to create copies that are automatically edited in the same way as the original event.
You can convert a shared copy to a real copy by selecting Edit > Functions > Convert to Real Copy. This creates a new version of the clip that you can edit independently. The new clip is automatically added to the Pool.