When the bullet does not want to sit on the case because it is too short to get flared, I stop and pull it out. This is not optimal because by then it has a primer in it, but that is what I have been doing. I am using a separate flare die on the 650, do not know if the Dillon measure would flare them.
I have been using the sorters before I load on my 9mm brass for two reasons, I use the 40 pan to catch any 40 or 45 cases, and then the 9mm pan to shake out any stones. The number of 9mm cases that makes for a good quantity for sifting out the stones is just about the right amount to not overload the feeder. Perhaps I might finally spring for that 380 plate...