Kiev have been charged over a pitch invasion by supporters who also set off fireworks during the last-32 second-leg game against French club Guingamp in Ukraine on Thursday.
Inter and Celtic were also charged after fans let off fireworks during their return match in Italy.
"We have to acknowledge ... scenes of violence and racism in and out of the stadiums that neither UEFA nor any true football fan can tolerate," said UEFA general secretary Gianni Infantino at the draw for the last 16 on Friday.
UEFA has yet to decide whether it will take action against Feyenoord or AS Roma after their clash in Rotterdam was suspended for more than 10 minutes when objects were thrown on to the pitch, including a giant plastic banana.
Inter will meet VfL Wolfsburg in the last 16 while Dynamo take on Everton and Roma face Serie A rivals Fiorentina.
European football's ruling body UEFA is also investigating an incident where Bayer Leverkusen supporters displayed an illicit banner during the Champions League last-16 first leg against Atletico Madrid in Germany on Wednesday.
(Reporting by Ed Osmond, editing by Tony Jimenez)
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