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To expand on the comment I left on your question, in the Nazi regime's early days (and in the run up to it), a few judges thought it was a good idea to condemn nazis who overstepped, only to see the offenders getting pardoned on the spot. They learned what they shouldn't bother prosecuting in short order. Here's one example:
In August of 1932, in the town of Potempa, nine Nazi Stormtroopers murdered a supporter of the German Communist Party, kicking him to death in his own apartment as his family watched in horror. Six were convicted, with five receiving the death penalty.
After the verdict, Hitler sent them a telegram in which he declared to them his "boundless loyalty."
Shortly after he came to power in 1933, he pardoned the killers.
This continued on into WW2, going as far as overriding military courts:
De Mildt contrasted the experience of Täubner in postwar German courts with that of an army officer Manfred Blume, who during the summer of 1942 randomly killed a number of Soviet prisoners of war by shooting, beating, and bayoneting. A military court sentenced him to two years in prison plus demotion for manslaughter. Hitler, however, quashed the sentence and terminated the proceedings, opining that one cannot reproach “vital natures” in the unique fateful struggle of the German people, who reject all humanitarianism. Ironically, Hitler’s appreciation of Blume landed him in enormous trouble. Instead of the relatively privileged convict status of a somewhat overzealous military officer, Blume took charge of a battalion at Stalingrad, and was taken prisoner and sentenced in the USSR to twenty years forced labor.
This article might have a few more examples - I couldn't access it, but the Google snippet seemed very promising.
Anyway, the short answer is yes: there were courts - both civil and military - who convicted nazis for going too far; but then the criminals would get pardoned by Hitler.
Upvote:1
In 1943 General Feketehalmy-Czeydner was convicted by the Hungarian Courts for 15 years for the mass murder in Novi Sad. During the German occupation in 1944 Hitler had let him loose after which Czeynder joined the Waffen SS. After the war he was hanged in Serbia, see https://en.wikipedia.org/wiki/Ferenc_Feketehalmy-Czeydner