The England international caught opposition striker Danny Ings with a boot down the back when racing out during the second half of the Toffees' 2-1 win.
Hughes claims that Ings got to the ball first and Pickford should therefore have been given his marching orders, a week on from Phil Jagielka being dismissed for a challenge on Diogo Jota.
"Their keeper should have been sent off for the challenge on Danny," he told reporters at his post-match presser. "They had a man sent off for less last week.
"You saw the state of Ings' shirt. He had five welts on his back. Clearly there is contact. The referee was there. The linesman has a lot of experience. My assistant has been in to see the referee. We will look back on it, I didn't feel he needed to follow through."
Southampton had five players booked all afternoon, while no Everton players were cautioned.