A multiclass ranger (urban ranger) 6 / rogue 3 should have a trapfinding bonus of either +3 or +4, depending on whether the abilities stack. However, PCGEN is applying a total bonus of +16, apparently (according to the troubleshooting sheet) calculating the bonus as +8 - double what the bonus should be if they stack - and then applying this incorrect bonus twice (the +8 bonus is the one listed in the trapfinding description, the +16 one is the one actually being added to the skills). This can probably be corrected by editing the trapfinding instance used by the urban ranger.
The quick patch I ended up using:
Replace the definition of the rogue's trapfinding ability (in cr_abilities_class) with [this change may not actually be necessary]:
Also, replace the definition of the Urban Ranger's trapfinding ability (in apg_abilities_class) with:
There may be similar bugs in other places though.