Lille appeared to consider walking off in protest
Ryan Giggs scored from a free-kick as Lille were still lining up a wall.
The French side appeared to contemplate leaving the pitch in protest after referee Eric Braamhaar allowed the goal to stand.
Uefa will discuss Lille's protest and the behaviour of their players during the match on Friday.
On an incident-filled evening, United fans were involved in a crush scare in the Stade Felix-Bollaert and Uefa's control and disciplinary body will discuss the safety and security issues on 22 March.
Giggs' goal came seven minutes from the end of the match, giving United a 1-0 advantage ahead of the second leg at Old Trafford.
Lille president Michel Seydoux insisted his players would not have walked off the pitch.
"It was not an attempt to get the game abandoned - it was an emotional moment," said Seydoux.
However, United boss Sir Alex Ferguson branded Lille a "disgrace".
He added: "I have never seen that before in all my years in football.
"The Lille staff encouraged their players to come off and that made it a hostile atmosphere inside the ground. It's a disgrace."
The first leg of the round of sixteen in the  was completed on Wednesday, with at least one controversial result, and a bag full of ties.  The leg began on Tuesday with four games, and the other four were played the next day, including reigning champions FC Barcelona of Spain.

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