Even in the absence of external influences the operability of a quantum computer (QC) is not guaranteed because of the effects of residual one- and two-body imperfections. Here we investigate how these internal flaws affect the performance of a quantum controlled-NOT (CNOT) gate in an isolated flawed QC. First we find that the performance of the CNOT gate is considerably better when the two-body imperfections are strong. Secondly, we find that the largest source of error is due to a coherent shift rather than decoherence or dissipation. Our results suggest that the problem of internal imperfections should be given much more attention in designing scalable QC architectures.