Scientists don't work with the wrong model of reality. Different models may have boundaries of applicability, within these boundaries everything is correct and reproducible. For example, Newtonian physics works great with objects common to our life, but it cannot be applied, for example, to describe elementary particles or near-light speeds. For gases, for example, in some framework, the Mendeleev-Clapeyron equation can be applied, but for more complex cases it is not applicable.
In general, the task of science is to compare theory with practice, watch, where simpler calculations can be applied, and where more complex ones.
Because contradictions arise when other models appear, which contradict the old ones in the opposite direction. With the progress of progress, some theories are eliminated, some merge together, forming a clearer understanding of the universe. On the path of development of science, contradictions are inevitable, but their very presence and the search for possible solutions form the process of cognition.