Errors of this kind are transfer errors, where (for software) the image loaded onto the vehicle is not bit-for-bit identical to the original code. I would agree with the assessment that these errors are rare, since verification of the process is rather easy: all firmware update procedures already have an established process for verifying the written ROM contents.

What they're actually saying is that most navigation errors will stem from design flaws, not from bit-flip errors, which seems a defensible assumption to me.