Memristors are receiving a growing attention for many different application areas in computer engineering. Besides replacement for main memory and storage class memory they can also be used as configuration memory in FPGAs. Unfortunately, memristors will not be 100% defect free. This paper first categorizes the different types of errors that memristors can exhibit. Then it is shown how configuration memory can be built in FPGAs using memristors. Using these defect types and configuration memory implementations, the influence of these defects on the operation of FPGAs is analyzed. We carry out this novel analysis with respect to logic implementation and with respect to the routing architecture. It turns out that the respective choices of current FPGAs are not well suited for memristor based configuration memory since even 1 % defect rate among the memristors prevents successful implementation of any of our benchmarks.