OK, I do not know if there is a solution to this problem although it is a problem in my opinion. I do not remember this happening 10 years ago although I find it happens frequently these days. When loading a person into Indy or HM that requires extra time to get in and out (which seems like every few cars these days) this requires a ride stoppage which in turns stops all the guests cars or doombuggies on the attraction, this is very distracting and happens a lot!
Now of course people who need more time to get in and out of a car due to a physical or mental handicap should of course be accommodated although there must be a more creative or effective way of loading and unloading these guests without requiring a general ride stoppage.
I have had this happen on a number of different visits when the ride would stop before the rolling ball scene and we would be sitting there for a few minutes with nothing happening. Sometimes the ride stops in a dark portion of the ride and the engine just idles.