Common sense is based in linear thinking. It is susceptible to cognitive bias and preconceived opinions that we form. I experience A, therefore I can directly explain it by B.
Common sense is actually a pretty bad indicator of truth. Because of cognitive biases and preconceived opinions, ideas that sound right are often wrong. “Common sense is actually nothing more than a deposit of prejudices laid down in the mind prior to the age of eighteen,” Einstein presumably said. (rule of thumb: always be skeptical with Einstein quotes!)
Asking who is right misses the point, although surely the person using tools can see further into the nature of things. Indeed, to see more clearly what makes up the world and, in the process to make more sense of it and ourselves is the main motivation to push the boundaries of knowledge.
See also: Networked thought