When Jiro is on the train after learning that Naoko is sick, he has tears running down his eyes.
Kayo chewing out Jiro for being away from his wife to design his plane before breaking down crying saying that she sees Naoko as a sister and will eventually perish from TB, for she has seen the tragedy firsthand, being a doctor and all.
Kayo seeing Naoko walking down the road, then finding a letter saying she's going back to the sanatorium to die so she can spare Jiro the pain of seeing his her dead.
Jiro sensing the changing wind after the successful test flight, realizing that his wife is gone. He is unable to respond to the praises of the test pilot and his bosses.
Jiro's last dream, where in the ashes and rubble of the war from which his planes were used, he meets with Caproni to discuss how his dreams were realized before seeing Naoko one last time.
"Hayao Miyazaki's Final Masterpiece" can come off as this in a meta sense.