One problem related to clutch pedal/linkage has been reported for the 2016 Jeep Wrangler. The most recently reported issues are listed below.
Vehicle has developed a rattle in the clutch/transmission assembly. Searches for other people affected by this yield numerous reports of clutch throw out bearing failures. It affects shifting and clutch engagement negatively. Makes it hard to positively engage shifts at speed. Mine has not yet failed but the dealership and Jeep have both been very resistant to acknowledge a safety issue that clearly affects numerous manual transmission Wranglers dating back to ~2008. A personal acquaintance also had a clutch throw out bearing fail on the highway (same make model and year vehicle). He is currently pursuing replacement of vehicle after massive damage done from throw out bearing failure. Please be aware that my vehicle had already had the shifter replaced (recall failure). This issue is separate from the shifter linkage recall. I've attached some documentation below (a small sampling of the users who are experiencing this issue for years).