Oh, in the extended edition it shows KGBeast (Luthor's head henchperson, he's never called that in the film) burning all the corpses with a flamethrower to make it look like they were killed with heat vision.
The super-distinctive Lexcorp bullet thing makes no sense, though. It was like they needed a clue for Lois Lane to follow to tie it to Lexcorp, but in the end Lex just kidnaps her right as she's figuring it out, so it was kind of pointless anyway. And it makes Lex look dumb, because he uses distinctive Lexcorp bullets to frame Superman.
It would've made more sense if Lex had used some plot device bullet that's designed to disintegrate or explode when it hits a target - so that it's slightly more plausible to accuse Superman of killing the people in Africa, since there'd be no bullets in the bodies - and she picks up an un-disintegrated round that got lodged in her notebook and later ties it to Lexcorp, who designed this weird leaves-no-evidence bullet.
One other idea I had was that the bullets were made out of Kryptonian metals and designed to hurt or kill Superman, and Luthor used them because he knew that then the US military wouldn't investigate too closely because they didn't want to publicly admit that they hired Lexcorp to design anti-Superman bullets. But again, none of this is in the film, and it suffers for it.