typeof(List<>) is an example where they differ. The property returns an empty array, while the method returns an array with a generic T in it. (this T has IsGenericParameter true)
From reading the documentation, I think that you can think of GenericTypeArguments as GetGenericArguments().Where(t => !t.IsGenericParameter).ToArray(), i.e. only the concrete types. See also ContainsGenericParameters.