Romania face action after fans set off fireworks and threw objects, with Albania accused of the same offences in addition to allowing a pitch invasion.
The charges mean that eight of the 24 teams competing in the tournament are the subject of disciplinary probes.
Albania won the Group A match 1-0 to maintain slim hopes of progressing while eliminating Romania.

Cavendish, 30, is looking for more qualification points at the event in Germany from 28-29 August in order to compete for GB in the omnium in Rio.
Coach co-ordinator Iain Dyer said: "He made a very promising start back on the track in Derby and he'll be looking to continue building on that form."
Cavendish won the Madison with Bradley Wiggins at the Derby Revolution.

Drifters was made in 1929 by acclaimed Scottish documentary-maker John Grierson.
It shows fishermen harvesting shoals of herring off Scotland's east coast.
East London-born sound artist Jason Singh will provide vocal sound effects during screenings of the film in Lerwick, Helmsdale and Anstruther.
The tour, called Following the Fleet, is supported by the National Lottery through Creative Scotland and also by Film Hub Scotland, which is part of the British Film Institute's Film Audience Network.
Between 31 August and 18 September, the film and performances will be held at venues in Baltasound and Lerwick on Shetland, Stromness on Orkney, Helmsdale in Sutherland, Aberdeen and Anstruther.
Singh, who will also deliver workshops on beatboxing and other sound effects for secondary school pupils at the venues, said: "I'm really excited about the Following The Fleet tour.
"I am keen to see what people will make of a live beatboxed score to a silent film.
"I'm also really looking forward to running workshops as it will give people the opportunity to explore their own voices in new ways and it will also give me the chance to meet, share and explore with new communities and cultures."
Uefa has opened proceedings against Albania and Romania after incidents in Sunday's Euro 2016 match in Lyon.
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Mark Cavendish will continue his bid to gain a track place at the 2016 Olympics by riding at the Dudenhofen GP.
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A silent film made 87 years ago about Scottish herring fishermen is shown at venues across Scotland accompanied by performances by a beatboxer.