Most of the time, no. According to the international laws (more specifically, the Hague Conventions of 1907 which Germany signed and Nazi Germany respected), only the execution of lawful combatants was a war crime.
Hague Conventions define the lawful combatant as the one who (1) wears the insignia unambiguously marking him or her as a member of the Armed Forces – which include guerilla units; (2) openly carries his or her weapons; (3) is a member of a unit commanded by a designated individual (commanding officer) and (4) conducts military operations in accordance with the laws and customs of war as defined in Hague conventions.
Resistance fighters on German-occupied territories undoubtedly were heroes and patriots, but, alas, in most cases they violated one or more of these requirements. Therefore, according to the Hague Conventions they were unlawful combatants (i.e. war criminals).
Consequently, German occupation authorities had every right to prosecute these unlawful combatants and punish them according to wartime laws. Which usually meant death by hanging or by a firing squad.
However, when Resistance fighters did follow the rules of the Hague conventions and were executed by the German authorities nevertheless or sent to concentration camps instead of POW camps (and it happened), the authorities in question committed the war crimes themselves.
It should be noted that German occupation authorities usually had a “zero-tolerance” policy towards common criminals on occupied territories. Consequently, they ruthlessly and immediately executed pickpockets, burglars, rapists, robbers and other common criminals.
Consequently, not everyone executed by German military authorities in occupied territories (or sent to concentration camps) was a Resistance fighter, a hostage or a completely innocent victim.