Limitations of the Scientific Method. Clearly, the scientific method is a powerful tool, but it does have its limitations. These limitations are based on the fact that a hypothesis must be testable and falsifiable and that experiments and observations be repeatable.This places certain topics beyond the reach of the scientific method.Science cannot prove or refute the existence of God or any other supernatural entity.hese limitations are based on the fact that a hypothesis must be testable and falsifiable and that experiments and observations be repeatable. This places certain topics beyond the reach of the scientific method.