-SPOILER- The most significant addition is a 30-second scene where it's revealed that Officer Weaver was deeply involved in the events that transpired before the movie, basically implicating him for much of what happened. The PG-13 omits this twist entirely.
When Ryan stabs Officer Weaver toward the end of the movie, Weaver says, "I protected you all these years", clearly implying that he was involved in the events that transpired before the movie. That statement by Officer Weaver is in the PG-13 version of the movie, so while it may not be complete, it is not omitted entirely.