One problem related to engine exhaust system has been reported for the 2006 Jeep Commander. The most recently reported issues are listed below.
I own a 2006 Jeep Commander and I have had to take it in to have the bolts in the manifold replaced three times now. We bought the Jeep brand new in Aug. 06. The first time the bolts broke were in may 08, the 2nd time was July 09 and now Apr 10. The first time the bolts broke the Jeep was under warranty, the other 2 times I've had to pay out of pocket for the repairs. We drive the vehicle for everyday use and there should be no reason for these bolts to keep breaking. I have called Chrysler to let them know about it, but got no where. The first incident I had one broken bolt, the 2nd time there were 3 bolts broken and this time there are 2 broken. We have owned many cars and never once had to replace bolts in the manifold until purchasing this Jeep. My mechanic tells me that bolts breaking off in the manifold is not a normal thing that should be happening. The Commander we own has an 8 cylinder engine in it.