No. This is a common misconception among both small and medium businesses. Taking a research credit on a timely filed return, including extension, does not increase your company’s audit risk. According to IRS statistics, only 0.9% of corporate tax returns and 0.2% of small businesses (S-corp and Partnerships) are selected randomly.
According to IRS guidelines, a return can be selected for audit based on a myriad of reasons. There is no directive that targets companies specifically who claimed R&D credits.