Rehabilitation exercises cause fatigue because tasks are repetitive. Therefore, inevitable human motion performance changes occur during the therapy. Although traditionally fatigue is considered an event that occurs in the musculoskeletal level, this paper studies whether fatigue can be regarded as context that influences lower-dimensional motor control organization and coordination at neural level. Non Negative Factorization Matrix (NNFM) and Detrended Fluctuations Analysis (DFA) are the tools used to analyze the changes in the coordination of motor function when someone is affected by fatigue. The study establishes that synergies remain fairly stable with the onset of fatigue, but the fatigue affects the dynamical coordination understood as a cognitive process. These results have been validated with 9 healthy subjects for three representative exercises for upper limb: biceps, triceps and deltoid.