1. The situation will happen if you did not move the ball back to the time where two balls just collide. (If you just checked if those two ball collide with each other).
2. If you did the time correction. The situation you have descrbed might happened if the velocity was set too large or the time step is too large. And it also possible that you might have three balls collide at the same time (within your simulation time step).  However, the program only take care of two balls collision. Reduced the time step might help.

Because I do not know how it was implemented in your program and what are the initial condition for your case, I can not say any more.