Your logical data model should effectively capture the business requirements of your application. Your physical database design should be based on the logical data model combined with the necessary changes that you as a DBA feel are needed to maximize the efficiencies of your RDBMS.
If you are finding that you have to make numerous changes to the underlying database design through out the software development life cycle of your application it is indicative of two things:
- Scope creep - You're allowing new requirements to be introduced at an inappropriate time.
- Insufficient Business Requirements - You're data modeler(s) (or system analysts) did not sufficient translate the requirements from the business analysts. This resulted in an incomplete or incorrect data model to support the requirements of your application.
That being said once an application has been turned over to production it is not uncommon to have to go back and make iterative changes to the data model to support the natural evolution of the application or underlying business processes.
Hope this helps.