Leona might not have a line in the game about already doing everything the year before, but he does have a line from his alchemy lessons of, “I did this last year, too,” which seems like it would insinuate that he did repeat his third year in the game.
But he also says he “learned something new,” and that he caught a bird. It is a little unclear how canon the lesson lines are to the main story.
There is a part in the Main Story where Azul crafts a potion that appears on the third-year class’ final exams. Next year Azul will be able to say, “I did this last year, too,” despite how he will presumably not be repeating his second or third year.
It is possible that Leona, too, was performing third-year magic in his second year, especially considering how he canonically learned all of NRC’s curriculum before enrolling.
In the novel it was confirmed that the year Leona repeated was his second, but while the novels and game will sometimes share identical dialogue they are also sometimes completely different from one another, so a thing being canon to the novel does not mean that it is canon to the game.
“Jack had thought that his letter of acceptance from Night Raven College had been a once-in-a-lifetime-opportunity. He had never considered the possibility that he may compete with Leona one day due to their age difference, but then Leona had repeated his second year.”
– Twisted Wonderland the Second Novel (fan translation)
And here is a Twstsoku thread on this very topic:
It starts out with the announcement that Leona has been confirmed to have repeated his 2nd year, but there is someone towards the bottom who says that they also thought that it was his third year that Leona repeated, based on his labwear line.
So it seems not an uncommon interpretation that Leona repeated his third year. Is Leona repeating his second year only canon to the novel? Maybe, and maybe one day there will be a more solid confirmation from the game, and then we will know for sure.
Twisted Wonderland Reference Note 