From the opinion (pdf):

In this prefatory statement we should note that the rather lengthy sentences imposed on the defendants—eleven years and a day and twelve years respectively—result primarily from their convictions under § 924©. Why?

Because Congress directed a mandatory minimum sentence of ten years for all defendants convicted under this statute, i.e., using a gun in relation to the commission of a crime of violence. The underlying crime of violence with which the defendants were charged is assault within the special territorial jurisdiction of the United States. Once the defendants were charged by the government and convicted by the jury under this statute, the district court had no discretion but to impose at least a ten-year sentence. Thus, the sentences in this case reflect the mandatory ten years for violation of § 924©, and one year and a day and two years, respectively, for the remaining several convictions.

As to the Government's evidence:

The government’s evidence showed that the agents had no reason to shoot the drug smuggler —that he had abandoned his van loaded with marijuana, that he was running on foot back to Mexico, that he posed no physical threat to either officer, and that he was shot in the buttocks. It is well established that the Fourth Amendment to the United States Constitution does not permit officers to shoot a fleeing suspect unless the suspect poses a threat to the physical safety of the officers or to the public.

The agents' evidence:

They testified that they saw something appearing to be a weapon in the drug-smuggler’s hand, that the situation was tense, that they felt in danger, that they acted as reasonable officers in pursuit of a possibly dangerous drug smuggler, and that firing a weapon was justified.Furthermore, they testified that their failure to report the incident was only a matter of negligence.

As to Aldrete-Davila, the drug runner who got shot:

Aldrete-Davila is a drug trafficker. On the day he was shot, he had agreed to transport drugs already located in the United States. He illegally crossed the border on February 17 in order to reach a van that he had agreed to drive. The van was parked near Fabens and contained a large load of marijuana. The keys to the van were already in its ignition, and Aldrete-Davila began driving it towards Fabens.

The agents spotted the van, a chase ensued, the van got stuck in a ditch, and Aldrete-Davila was shot. His version:

Aldrete-Davila denied turning around and denied having any object in his hand. He instead insisted that he simply ran towards the border, saw dirt being kicked up around him by bullets, and then fell, feeling a burning sensation in his left buttock. He testified that he waited for Ramos and Compean to arrest him, but saw them turn away. Aldrete-Davila eventually made it back over the border. He was apparently met by the drug traffickers for whom he was working and was taken to a medical facility. The bullet fired by Ramos had fragmented, severing Aldrete-Davila’s urethra.

As to the crime: There was a cover-up:

After the incident, there was a “cover-up”—including a clean-up of the area of spent shells and a failure by the two agents to report the weapon-firing incident, as plainly required by well-established Border Patrol policies.

The charges:

The indictment charging Ramos and Compean enumerated twelve counts. These counts included charges for attempted murder, criminal assault, unlawful discharge of firearms, tampering with official proceedings, and criminal deprivation of civil rights. After a lengthy trial, Ramos and Compean were found guilty on all charges save attempted murder, for which they were acquitted.

The Court reversed the convictions on five obstruction of justice counts relating to their failure to report the discharge of their weapons, finding that the initial Border Patrol investigation into what happened was not an official proceding.

But it upheld the convictions for assault, discharge of a weapon in the commission of a crime of violence (the assault) and deprivation of civil rights.

Returning to credibility and whether there was sufficient evidence to convict:

The defendants’ argument here is one to which they repeatedly return: they were justified in firing upon Aldrete-Davila. But, once again, we must remind the defendants that the jury did not believe the defendants’ testimony that Aldrete-Davila possessed an object in his hand.

Aldrete-Davila’s own testimony, the behavior of the defendants after the shooting, and the inconsistent testimony offered by both defendants and other Border Patrol agents allowed the jury to conclude that the defendants faced no credible threat and, consequently, there was no justification for their firing upon Aldrete-Davila.

Although disputed, the evidence, taken in the light most favorable to the jury verdict, supports the scenario that Aldrete-Davila fled toward the Mexican border after Compean took a swing at him with his shotgun and that, while he was in flight, the defendants without provocation fired their weapons at him several times.