CropEffect should inject the query factory, not an actual query instance

$container->get('entity.query')->get('crop')

This creates an actual query object which can only be used once. If someone somehow tries to use the same plugin instance twice, it fail will. Inject just the entity.query service and then all get('crop') on it.

Actually, since you already inject the crop storage, you can also just do $this->cropStorage->getQuery().