A little bit of common sense would dictate that cities that have virtually no hotel space would not have any late evening games, giving people time to get elsewhere after the game if they wish. Alas, UEFA, like FIFA, only request enough accommodation for visiting dignitaries and sponsors, and couldn't give a toss about traveling supporters.
Good point, it is a bit stupid that two of the four games there are 9pm kick-offs. However, it's only 45 minutes on the train from Lyon so it's probably not that much harder to get to than the new Lyon stadium. (And of course travelling supporters don't need to know NOW what extra trains they'll be running, do we? There's no rush, we'll just buy our match tickets and book our hotels and wait, don't worry about us.)
It's the same with Lens. It's only a short trip from Lille, but if you are there for a 9pm game (2 of 4 are), the last train back "handily" leaves at 8.50 pm