The function f contains a free reference to a variable called a. This is satisfied in some sort of global environment.

Later, f is called from a function in which there is a local a bound to 100. Of course, this a which is local to that function is invisible to the free reference in f which continues to refers to the global a that contains 10.

It could be there is some problem in R, but whatever that is, this article isn't exposing it in a convincing way.

Same thing in Common Lisp (using CLISP):

  [1]> (defun f (x) (* a x))
  F
  [2]> (setf a 10)
  10
  [3]> (f 3)
  30
  [4]> (defun g (y) (let ((a 100)) (f y)))
  G
  [5]> (g 3)
  30

(It could produce 100 if the symbol a were marked for binding as a special variable; but it isn't. Thus it's just a free variable in f resolved in the global environment, and a lexical binding in g).