Aliadiere, making his comeback from an ankle injury, chased a long ball into the box, and went down under a challenge from Morgan, prompting Boro's appeals for a penalty, but D'Urso gave a goal-kick.
Referee Messias was involvled in more controversy on 61 minutes when he pointed to the spot again when Baros went down under Taylor's challenge although he appeared to play the ball.
Zayatte was also involved in Everton's second goal as he was punished for a high challenge on Saha, who had expertly taken down a diagonal ball from Cahill in the box.