User errors are directly related to the expertise, the thoroughness, and the experience of the user. For a given user, these errors can only be minimized by good project management and thorough interaction with others. In case of inexperienced users, day-to-day interaction with a CFD expert/manager is required to avoid major quality problems. A structured work plan with intermediate results is important for intermediate and long-term projects.
A careful study of the CFD code documentation and other literature on the numerical methods as well as the physical models is highly recommended. Furthermore, benchmark studies are recommended to enable you to understand the capabilities and limitations of CFD methods. A comparison of different CFD methods is desirable, but not always possible.