You can try setting some validation rule in your entities for some fields to be unique, here’s a screenshot:
This way, mendix will not insert duplicated values.
Maybe, you should consider have a look at your microflows logic.
It’s not normal to insert duplicated with only 1 call, maybe there’s something on your logic that is causing this problem too.
If you use an entity in an import mapping, you will get a new object every time the mapping is called. If you don’t want that data to be persisted, you can use a non-persistable entity.
You can then determine whether you want to persist that data, and copy the attributes over to a persistable entity.
As others have answered, to prevent duplication you can use validation rules.