Recent IoT devices require extremely low standby power consumption, while a certain performance is needed during the active time, and Coarse-Grained Reconfigurable Arrays (CGRAs) have received attention because of their high energy efficiency. For further reduction of the standby energy consumption of CGRAs, the leakage power for their configuration memory must be reduced. Although the power gating is a common technique, the lost data in flip-flops and memory must be retrieved after the wake-up. Recovering everything requires numerous state transitions and considerable overhead both on its execution time and energy. To address the problem, Non-volatile Cool Mega Array (NVCMA), a CGRA providing non-volatile flip-flops (NVFFs) with spin transfer torque type non-volatile memory (NVM) technology has been developed. However, in general, non-volatile memory technologies have problems with reliability. Some NVFFs are stacked-at-0/1, and cannot store the data in a certain possibility. To improve the chip yield, we propose a mapping algorithm to avoid faulty processing elements of the CGRA caused by the erroneous configuration data. Next, we also propose a method to add an error-correcting code (ECC) mechanism to NVFFs for the configuration and constant memory. The proposed method was applied to NVCMA to evaluate the availability rate and reduction of write time. By using both methods, the average availability ratio of 94.2% was achieved, while the average availability ratio of the nine applications was 0.056% when the probability of failure of the FF was 0.01. The energy for storing data becomes about 2.3 times because of the hardware overhead of ECC but the proposed method can save 8.6% of the writing power on average.