15,000 traveling Besiktas fans resulted in heightened security around Lyon, but that hasn't stopped rival supporters from clashing in the streets, in the stadium and with police.
Objects were thrown and firecrackers let off before the kick off in France was delayed by the unrest and subsequent pitch invasion.
Players from both sides had emerged for the warm-up before the game when objects began to be thrown onto the pitch. "Kick off expected soon".
The trouble prompted police involvement outside the ground with French authorities allocating the fixture as "high risk" and commandeering 500 police for the fixture - more than double the number for a normal match. Defender Marc Bartra suffered injuries to his arm and wrist that required surgery.
Lyon won the match 2-1 courtesy of two late goals.
There was also trouble involving Leicester City fans when their team played a Champions League tie in Madrid in midweek.
A review of all Thursday night's Europa League action.
United opened the scoring at Anderlecht with a 36th-minute goal but wasted opportunities to double their lead and then conceded an 86th-minute equaliser.
"I believe that it must be above all a place where people must be able to come in peace to attend a game, a show".
Still, United will be favored to advance at Old Trafford next week after controlling much of the game in Brussels.
Manchester United took an away lead through Henrikh Mkhitaryan, the Armenian firing home from a tight angle after Marcus Rashford's effort was repelled.
It will be all to play for in the second leg in Genk after the Belgians lost an entertaining clash against Celta Vigo 3-2 in Spain.
Davy Klaassen's 23rd-minute penalty and shot in the 52nd from Justin Kluivert's cross were a poor reward for their dominance at Amsterdam Arena.