Answered: Scoring Zone Confusion

Is it true that any balls that a robot is touching or holding at the end of a match will not have those points counted against them??? During competition my alliance would keep pointing it out.

No, this is not true.
Please refer to the Clean Sweep game manual found on this page:
http://www.vexrobotics.com/vex-clean-sweep.shtml

Pay close attention to the definition of “scored”.