Juvencio Nava killed Don Lupe in his youth because Don Lupe killed one of Nava's animals for grazing on his land. His fear at being caught has driven him to run and hide for forty years, and he had finally started to relax his vigilance for a little bit of time. However, this relaxation causes him to take an unnecessary chance and try to stop his small corn plot from being trampled by soldiers; although Nava has time to run to the mountains, like all the times before, this time he goes to the soldiers and tries to stop them from ruining his crop:

He'd seen them for the first time at nightfall, that dusky hour when everything seems scorched. They'd crossed the furrows, trodding on the tender corn. And he'd gone down on account of that -- to tell them that the corn was beginning to grow there. But that didn’t stop them.
(Rulfo, "Tell Them Not to Kill Me!," Google Books)

This could have several interpretations. One is that Nava was simply tired of running and hiding, and despite his protestations to be spared, was ready to die and move on from his fear. Another is that he truly thought that enough time had passed so his crime would be forgotten; he did not realize that Don Lupe's son is now a Colonel who has been searching for the murderer all this time. In either case, Nava is caught because he makes the decision to confront the soldiers rather than run from them.