Several flares were thrown onto the pitch from the section where the 3,000-strong travelling Galatasaray supporters were located towards the end of the first half at the Emirates Stadium, causing the Group D match against Arsenal to be briefly halted.
At St Jakob Park, a battery appeared to be thrown in the direction of the assistant referee near to the Basle goal during the tie with Liverpool, while at Anderlecht's stadium, flares were lit in the area housing travelling Borussia Dortmund fans.
If found guilty, the clubs could be hit by a fine from the European governing body, or be ordered to play matches behind close doors.
A statement on UEFA's website read: "D isciplinary proceedings have been opened following incidents at last night's UEFA Champions League matches:
"Match: UEFA Champions League Group B match between Basle and Liverpool (1-0) played on Wednesday 1 October in Switzerland.
"Basle: Throwing of missiles (art
16 (2) (b) DR)
"Match: UEFA Champions League Group D match between Arsenal and Galatasaray (4-1) played on Wednesday 1 October in England.
"Galatasaray: Crowd disturbances (art
16 (2) (f) Disciplinary regulation); setting-off and throwing of fireworks (art
16 (2) (b) & (c) DR)
"Match: UEFA Champions League Group D match between Anderlecht and Borussia Dortmund (0-3) played on Wednesday 1 October in Belgium
"Borussia Dortmund: Crowd disturbances (art
16 (2) (f) Disciplinary regulation); setting-off and throwing of fireworks (art
16 (2) (b) & (c) DR)
All three cases will be dealt by the UEFA Control, Ethics and Disciplinary Body on October 16.
Source : PA
Source: PA