The swirl flaps sit in the intake of both cylinder banks, and a central electric actuator moves them through a linkage. Soot builds up on the linkage and on the flaps, the flap starts to bind, and in the end the plastic breaks. This is the most frequent single failure on this engine, and the broken pieces can get into the engine, which can lead to engine damage. The symptoms are the engine warning light, rough running and a lack of power, with the code P2004 or P2005 in the fault memory. The condition of the flaps can be seen with an endoscope through the intake, without dismantling. It is worth looking above 150,000 km, especially on the W164 ML320 and ML350 CDI. An aluminium repair kit is available for it, which lasts longer than the factory part.

In the Mercedes 7 speed 722.9 automatic (7G-Tronic / 7G-Tronic Plus) the mechatronics unit and the conductor plate (Leiterplatte) age over time: jerking on shifts, delayed engagement, a "Getriebe schützen" message, and fault codes on the gearbox electronics.

The Mercedes 5 speed 722.6 automatic (5G-Tronic / NAG1) has three faults that also recur on the used market: (1) the control electronics sit inside the gearbox housing, and a leaking connector lets oil onto the electronics; (2) cooling faults around 2003 (and later) can let antifreeze into the ATF, which shortens its life; (3) wear of the torque converter lock-up clutch contaminates the valve body and causes jerky shifts.

The oil cooler sits in the V between the cylinder banks, and its seal becomes porous over the years. The leak is characteristic: there is no visible trace on the outer sides of the engine, because the oil collects in the V under the intake and drips down from there. A smaller oil puddle can therefore appear under the car, while the place of the leak cannot be found from outside. As the fault gets worse, oil can also get into the coolant, and that shows up as oily streaks in the expansion tank. It gives no fault code. The repair is expensive because the cooler can only be reached after removing the intake and the swirl flap actuator. In a specialist workshop it can run up to 2,000 euro. The fault comes up above 120,000 km. One thing is worth asking even after the repair. If the V is not cleaned out thoroughly, the remains of the old seal and the soot get into the oil circuit, and there they can ruin the bearings and the oil passages as well.

Combustion gases escape past the shaft of the Bosch piezo injector, and soot builds up around the shaft. The symptoms are a hard, rough cold start and a rough idle. The engine has six injectors, so finding the faulty one is more work as well. The quantity correction values of the control unit have to be read per injector, and this is worth doing before anyone replaces all of them. A cleaning additive and better quality fuel help to prevent the sooting. The fault comes up above 120,000 km. The high-pressure system of the same engine (Bosch CP3) can also give starting trouble and a lack of power at high mileage, so the diagnosis separates the two.

The maker issued recalls and voluntary service actions for the six cylinder OM642 diesel, aimed at defeat devices (Abschalteinrichtungen) in the engine control software.