One problem related to clutch pedal/linkage has been reported for the 2012 Jeep Wrangler. The most recently reported issues are listed below.
My 2012 Wrangler sport (6sp) has a faulty transmission. It makes a horrible rattle at high rpms in 3rd and 4th gear, the gears whine and 1st is really hard to engage when the vehicle is slowly rolling. Sometimes I have to double clutch it just to get 1st gear to work when rolling. Reverse grinds. The gear shifter shakes excessively when vehicle is in 4th and 5th gear. Shifting from 1st to 2nd is notchy as is 5th to 6th and when putting it into reverse. The clutch often has a crunchy feel when I press the pedal to the floor.