I've noticed this also. I have four real-time teams and I checked my catcher's stats.

I have Darrin Fletcher and Damian Miller catching on one team. Fletcher had 10 Passed Balls in 113 games but in PB he already has 16 in 68 games. Miller had 11 passed balls in 86 games and now has 14 in 44 PB games.

I have Piazza on the other three teams. He had 7 passed balls in 137 games for the Mets. On my teams he has 14 in 98 games, 9 in 91 games, and 6 in 95. Seems the PB rate of occurrence is much higher than in real baseball. Note that if you call up a players real stats in Purebaseball, The PB column in the defensive stats section is not passed balls. I guess its some sort of defensive rating.