Harry- the patch or wads are always behind the ball or shot so the projectile is registered only. When shooting shot over the chronograph, I remove the rods and place a board in front of the chronograph with a virtical red or black arrow indicating the eye location. The board doers pick up the odd shot which might have badly damaged the chronograph. Shot hitting the wires may rip them from the plastic holders and that wouldn't be a good thing.
As you know, time to time you'll get a wonky reading - such is normal with most any chronogrpahs when shooting most calibres. I've used Oehler, Pact and several Chrony's - all have given virtually identical results. Funny thing, is I never got a 'bad' reading when shooting the very large 'bore' guns, BP or smokeless.