Bayern fans raised a banner saying 'without fans football is not worth a penny' at the Emirates
Before the match, travelling Bayern fans held up a banner which read: "without fans football is not worth a penny" to highlight the cost of ticket prices and then once the action started toilet roll was thrown onto the pitch, which caused a delay as the debris was removed.
During the closing stages, there was also a brief disruption when a supporter ran on to the field and was eventually taken off by stewards after stumbling to the floor.
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A statement from UEFA said: "Disciplinary proceedings have been opened following the UEFA Champions League round of 16 match between Arsenal FC and FC Bayern Munchen (1-5), played on 7 March in England.
"Charges against Arsenal FC: Field invasions by supporters – Art. 16 (2) of the UEFA Disciplinary Regulations (DR)
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Objects were thrown on the pitch at the beginning of the match at the Emirates stadium
A supporter made his way onto the pitch towards the end of the game
"Charges against FC Bayern Munchen: Throwing of objects – Art. 16 (2) of DR.
"No other disciplinary cases have been opened after this match."
Both clubs could be hit with fines as a result.