That's not necessarily a off-by-one error, but a broader problem of audio synthesis, which you can generally deal with by applying low pass filtering. For example depending on starting phase of a sinus oscillator multiplied by a simple linear volume envelope (1.0 -> 0.0) you will get a click at the first sample, which is loudest at multiples of pi/2 for the starting phase (cos). So you need to low pass filter the envelope to get a quick fade-in of the oscillator without click. How you do this and how that sounds is up to you. The original hammond organ similarly got some nice analogue clicks as initial transients because of this 'problem' as a side effect btw, in digital its much harder and expensive to make nice curves. De-clicking an audio engine properly is certainly an important and sometimes frustrating task.