Footage from the fourth-round tie at Old Trafford shows a green light appearing on United and England captain Rooney's face as he prepared to take his kick in the penalty shoot-out at the end of the contest.
Rooney's effort was saved by Boro goalkeeper Tomas Mejias as United were beaten 3-1 in the shoot-out following a 0-0 draw after extra-time.
The FA said on Thursday it was aware of reports of the incident and was looking into the matter.
The penalties were taken at the end of the ground housing Boro supporters, with around 10,000 away supporters in attendance.
Source : PA
Source: PA