Were these the two guys who shot the running Mexican who left all the pot and then tried to cover it up and didn't report it?
They were accused and found guilty of what you stated. Here's another synopsis as stated in this commentary:
Border officers' case is travesty of justice
http://www.statesmanjournal.com/apps/pbcs.dll/article?AID=/20060827/OPINION/60825046/1049
U.S. Attorney Johnny Sutton, a Bush appointee, prosecuted the agents. In March, a jury found them guilty of assault with a dangerous weapon, discharge of a firearm during a violent crime, obstructing justice, lying about the incident and willfully violating Aldrete-Davila's Fourth Amendment right to be free from illegal seizure.
With their supervisors on site, did they feel that they were covering anything up? Since they didn't think anyone was shot and it was observed by their superiors, I don't expect they thought it was a coverup.