Play had to be stopped momentarily during Galatasaray's 4-1 UEFA Champions League defeat at Arsenal on Wednesday, when fans hurled flares onto the Emirates Stadium turf.
Wesley Sneijder - captain in place of the unwell Selcuk Inan - made his way over to the Turkish fans in a bid to halt the unrest, with action resuming soon after.
Proceedings have also been opened against Dortmund for similar offences during their 3-0 win at Anderlecht, with UEFA citing the "setting-off and throwing of fireworks".
Basel - 1-0 winners over Liverpool - are facing punishment after missiles were thrown onto the pitch.
All three cases will be dealt with by the UEFA Control, Ethics and Disciplinary Body on October 16.
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