Speaking ASA
There is no rule preventing this from occuring. As long as you are ready to play ball when the pitcher has completed his/her warm ups.
Ramification if not: Rule a ball on the batter for each additional ball thrown by the shortstop after you are prepared to play ball (a la additional warm up tosses) or charge the defense with another conference. However, that may delay the game even further if thay have none available
A little preventive umpiring handles this quite well. Just as you would when one team utilizes their opponents charged conference to conduct their own, when the pitcher gets to the next to last warm up toss, a simple, but stern, "okay, lets go!" will usually do. By the time you get back behind the plate, the defense should be ready to go.