The Reds succumbed to defeat in Naples after Lorenzo Insigne's late strike sent Carlo Ancelotti's side to the top of Group C, a point ahead of Liverpool and Paris Saint-Germain.
Following the game, the Italian side have been charged by European football's governing body for breaching disciplinary regulations.
They have been charged due to fans setting off flares in the home end, as well as stairways being blocked during the game - in direct contravention of article 38 of the UEFA Safety and Security Regulations.
There was also trouble in the other Group C fixture between PSG and Red Star Belgrade, during which Thomas Tuchel's side ran out 6-1 winners with Neymar scoring a hat-trick.
The French side have also been charged for their supporters setting off flares and additionally for crowd trouble.
Meanwhile, Red Star Belgrade also face charges over crowd trouble and for possible "illicit chants" from Serbian supporters.
The cases will be heard by UEFA on October 18 and may result in a ban or strict restrictions in future games.