UEFA also cited organisational issues such as blocked stairways.
The cases will be dealt with by UEFA's disciplinary body on May 21.
Dnipro reached their first European final when striker Yevhen Seleznyov's header gave them a 1-0 win over Napoli in the semi-final, second leg on Thursday to complete a 2-1 aggregate success.
They will face Sevilla in the final on May 27 in Warsaw.
(Reporting by Toby Davis in London; editing by Ed Osmond)
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