Despite the accepted answer, I think the more obvious answer is that this is just a (self-referential) joke.
So most likely Indiana Jones never actually learned to fly a plane, he kept one in the air in Temple of Doom (which technically checks the "flying" part), but he obviously botched the landing. So he answers truthfully: Fly? Yes. Land? No.
Now explaining jokes is always funny, but that actually works as a short standalone sketch and if you've seen Temple of Doom, you'd also get a nice throwback to that adventure.
Now with regards to that Lost journal of Indiana Jones. That was apparently released in 2008 for the Crystal Skull movie so not sure that should count as canon with regards to the original trilogy.
But if you consider it canon and consider that many people (maybe even the writers of this log) don't actually realize that Temple of Doom is actually a prequel and not a sequel to Raiders of the Lost Ark. You might even include Raiders in that joke:
Like in "Raiders of the Lost Ark" he escapes the turmoil after the warrior temple with the help of his pilot, who has a pet snake(!). So as I'd imagine that wasn't a nice experience for a person with a snakephobia, that might be the origin of:
"Indiana comments in a to-do list that he must learn how to fly a plane."
Then in "Temple of Doom" he actually flies a plane but crashes it. Or in other words he can now cross "flying a plane" off the to-do list but instead:
Later on, he makes a new to-do list that includes learning how to land a plane.
You know the crucial part that he didn't consider last time.
While the "By 1938, he had learned how to fly a plane, but not land", probably has it backwards. 1938 is the in-universe year in which The Last Crusade takes place, so we know that he didn't learn to land until then ... well because of that very line of dialogue that you quote in the question.
So if you consider the chronological progression (Temple, Raiders, Crusade) then the lost journal doesn't actually make all too much sense here. Because if Indiana Jones would have really picked up flying AFTER Temple of Doom (he obviously couldn't fly in that adventure), he wouldn't have gotten far until Raiders we're he still has a pilot. But most crucially: Why would he have not gotten to the landing part by 1938! And I'm not talking about him being a slow learner, but about the fact that in Temple of Doom he literally had an experience that would have taught him that landing a plane is the most important part of all of flying.
So I'd suspect that the writers of that journal thought the progression is Raiders, Temple, Crusade and then made funny references to these three movies.