If you're asking why your MagnetoSpeed V3 gives you occasional errors, I'd be very surprised if it's due to wads or sabots, because those are not magnetic materials, and they don't produce any kind of electric current (every moving electric charge produces a magnetic field). So... unless you're using wads that have some kind of metal in them, I can't think of any way that wads or sabots might intereact with the magnetic sensors (most likely "Hall Effect" sensors) which are the heart of your chrony.
The one possible source of interference that I can think of is that hot powder gases streaming past the magnetic sensors probably contain lots of molecules and atoms that are electrically charged, and moving electric charges produce magnetic fields, so the hot gas stream will intereact with your magnetic sensors. Because the distribution of charged particles within the stream is probably at least somewhat different on every shot, it seems possible that every now and then the resulting gas stream magnetic fields will interfere with the magnetic field disturbance produced by the bullet, and generate an error.
EVERY sensor system of EVERY kind is also subject to noise of many kinds in its detectors, in its signal processing electronics, and in its operating environment. The hiss you hear in a stereo system when no record or tape or CD is playing is an example of noise in signal processing electronics. The flickering of fluorescent or LED lights is an example of operating environment noise that affects optical chronys. Errors in something like the chronys we're discussing here are often caused by noise of some kind. The ratio of signal strength (the magnitude of the detectable physical effect produced by a bullet as it flies downrange) to the sum of all the noise in the operating environment and detection system often determines the rate of errors and the limits of sensitivity. All of the detectable physical effects for the chronys we're discussing in this thread are pretty small (the shadow of a bullet crossing a photocell, the radio-frequency electromagnetic waves reflected from the base of a rifle bullet, the magnetic field disturbance caused by a bullet passing an inch or so from a Hall effect magnetic sensor), so I'm guessing that all of these chronys operate with small signal to noise ratios, and are therefore subject to at least occasional errors which don't seem to have any identifiable cause.