Neural confusion is a term, a metaphor if you will, that I use to explain what happens when you use exercises that attempt to isolate one muscle at one joint either to enhance performance or to prevent injury.
Let recognize that the brain does not recognize individual muscles rather it recognizes and organizes patterns of movement to take advantage of muscle synergies. Attempting to isolate an individual muscle creates “neural confusion” by sending mixed messages to the brain. Stop and think what happens in real life. Muscles work in synergies, in patterns to produce smooth efficient movement. That is the way we should train and rehab. Select multi-joint, multi-plane exercises that trigger efficient adaptable movements that transfer to performance. A simple rule of thumb is to integrate not isolate.