Just a small aside before starting, the Wehrmacht is the term for the German armed forces in all their branches, the Heer, the Luftwaffe, and Kriegsmarine. So when people talk of the crimes of the Wehrmacht, they do include that of the Luftwaffe and Kriegsmarine, though you're right in that the Heer holds the lions share of attention as they were the primary perpetrators of most crimes.
When it comes to the Luftwaffe's involvement in various war crimes, look no further than their strategic bombing campaigns, aptly named Terror Bombing for their intentional targeting of civilians in urban areas for the purpose of breaking enemy morale. The (in)famous Junkers Ju 87 Stuka dive bombers in particular were equipped with wailing sirens called the Jericho Trumpet, which you've probably heard in any given WWII movie, for the sole purpose of inciting panic among both soldiers and civilians during bombing runs to maximize chaos and deaths from the panic. Everywhere the Luftwaffe could reasonably reach with their bombers, terror bombing was practiced on all fronts, especially during the invasion of Poland, The Battle of Britain, and the invasion of the Soviet Union.
Luftwaffe guards were also stationed at many of the concentration camps along with the Heer and SS. Camps like Buchenwald, Auschwitz I and II, Monowitz, and Mauthausen all had Luftwaffe members among the guards and camp staff.
The Kriegsmarine also participated in numerous crimes while out at sea. The two largest crimes perpetrated by German sailors was leaving the survivors of Allied warships and merchant ships to drown after their ships were sunk, as well as actively shooting to kill survivors in the water. The most notable example of this was by Heinz-Wilhelm Eck, commander of U-852, who was convicted and hanged for ordering his crew to shoot survivors of the merchant vessels his U-boat sank.
If you want to read more, check out Terror From the Sky: The Bombing of German Cities in World War II by Igor Primoratz as well as World War II - War crimes & espionage by Karen Farrington