I'd venture a guess that about a third of my total runs that weekend had at least one cone.  A course design like this kind of makes that inevitable I believe.  
My fastest time of the weekend (47.638) had a tickled cone that negated it.  My cleanest fast time was a 47.909.  My first shootout run was a 48.2xx but had a cone.  Thankfully ( 

 ) I got a rerun on it due to a timing computer error and ran another low 48.xxx but still wasn't fast enough to advance.
The whole shootout format takes everything up another notch over a normal autocross and I'm still pretty new to it.  It is interesting to watch those that are very good at it in how they are maybe a bit cautious on their first few runs then let it all hang out when it gets down to the final 4.  It is not uncommon for even them to hit a cone and take themselves out.  
What makes this even more difficult than say an SCCA challenge is the competitor that gets to go second...knows if the car they are running against hit a cone or not before they run because there is only one car on the course at a time.