I'm probably one of the best people to answer this since I did the editorial prep for the trailer, and worked on the feature. (Zack has had us, the feature crew, involved in his trailers since 300. As was mentioned, more typically, feature crews aren't involved in trailers.)
Zod's dialog was taken directly from the feature dialog stem. In the film, Zod is transmitting this message to Earth. We left in the tone that you refer to because it worked well with the messed up, distorted nature of his transmission. I get that the trailer takes it somewhat out of context so it doesn't work in the same way. But, in short, it's not a mistake.
And @sound designer is right. The synth tone that @bryce mentioned is a sound that I came up with for the big Kryptonian weapon at the end of the film, that Junkie XL, one of Hans' close collaborators, integrated into the score throughout the film.