It's not that the sensors are disturbed...
The sensors stay still. But when an object travels at high velocity (it doesn't have to be at the speed of sound, or even that close), pressure waves build up in front of the object and form like a wake as it travels through the air. When these waves get tight enough, they can bend the light like a prism, making what's behind it seem like it's somewhere else.
After a few inches (depends on the speed, the higher the worse it gets), these waves dissapate. So given that the chrono measures from A to B and that distance is small, if the waves make it look like it's a tad shifted at sensor A or B, then it reads a false reading.
Here's an image showing the waves coming off a subsonic jet at ground level... you can see the distortion of the picture caused by them on the masts and close to the aircraft
and here's one i took... it's different from the heat haze and the sequence I shot showed these vortexes travelling
If you imagine a pellet is a small thing, travelling at similar speeds, if not greater, and this effect is quite apparent, then imagine the effect it can have on a small measurement over a small distance.
Putting a chrono downrange allows this wave to settle/dissappear and gives more consistent results. It's mentioned in my CED manual. A silencer/stripper may remove these, hence you get a different result.