Objective The jiggle of the motor evoked potential (MEP) induced by transcranial magnetic stimulation (TMS) depends on a number of factors including the assessment of this stochastic signal by the method known as area under curve (AUC). We aim to ascertain the MEP findings assessed by the AUC method obtained from individuals affected by lesions at different levels of the neuroaxis. Methods We systematically search and critically appraise the scientific reports publishing on the MEP obtained from individuals with hypo- or hyperkinetic disorders of the neural system, and dissect the neurophysical assessment of the obtained data. To accomplish this, we used the instruments named to as U-Pen Instrument for Neurometric Evaluation Uncommonly and Rarely Obtained from NeuroSignals 1.0 (UPINEURON 1.0), and the Quality of Assessment Statistics Index (QuASI). Results The MEP differences found by the classical peak-to-peak method decreased or disappeared when the AUC was used. The opposite was also true (Kappa = < 0.00). The internal consistency of the UPINEURON was 0.88. The mean of the UPINEURON 1.0 indicator was 34.8 (range = 16–50), and the mean of the QuASI scores was 56.5 (range 30–80). Spearman correlation between UPINEURON 1.0 and QuASI was 0.513. Conclusions The MEP jiggle found in individuals with disordered neural function is not a “minor” factor; it is beyond the underlying neural condition, sample size, type of coils, and number of trials, among other variables. The use of the novel indicators introduced in this investigation will help to improve the analysis of the AUC of neural signals. They may also lead to the reconsideration of current practices.