Lyon FC and Crystal Palace are owned by the same partnership group. They both qualify for the Europa League but due to the Multi- club ownership rules of UEFA both teams cannot play in the same competition if they are owned by the same group. One has to forfeit the competition for the other to play. Some people argue that Manchester City and Girona were allowed to play in the same UCL competition last season despite City football Group holding 44% in Girona shares and 100% in Manchester City, but the truth is that they placed their Girona shares on blind trust to be managed by an independent UEFA approved panel which secured compliance with UEFA rules and the both teams were allowed to play.
Same thing, or at least a similar thing, happened with Lyon. The owner put his shares in a trust somewhere else, so in theory Lyon should be able to get considered not his anymore. If City and Girona could, for the same thing, then we should be considered Lyon and Palace situation the same thing as well.
However, obviously they are not as big as City so they are not getting it done, people don't care about Europa league or Lyon or palace, so even if UEFA made a "bad" decision, the backlash won't be that big and Palace would be hurt and only Palace fans would dislike the decision. Normally, Lyon shares of his, is where it should be, and UEFA should allow both teams to be in Europa at the moment without much issues.