The output of plagiarism tools should only serve as a hint to look at a pair of solutions more closely. All judgement should be derived entirely from similarities between solutions and not some artificial similarity score computed by some program.
Unfortunately, this is not really what happens in my experience. The output of plagiarism tools is taken as fact (especially at high school levels). Without extraordinary evidence of the tool being incorrect, students have no recourse, even if they could sit and explain the thought process behind every word/line of code/whatever.