I've only seen the show as the DVD box set, so the original showing may have been different, but some of the scenes are subtitled, and some aren't. This doesn't seem accidental, or sloppy - like everything in the series, it has meaning and it adds to the development of the story.
The most powerful examples of this are two scenes with the Cousins.
At the end of S3 06, Gus meets the Cousins in the desert, in a very tense confrontation. It's not subtitled, but it doesn't need to be. We know the Cousins want to kill Walt, and we know Gus needs him alive, at least for the time being. They argue about it, Gus says something that makes them think... then he says Hank's name, very clearly. And we know that he's given them Hank, to kill, instead of Walt, and the credits roll.
The very next scene (the first scene of S3 07) is subtitled throughout. The Cousins, as small boys, squabble over a toy, and one (Marco) runs to their uncle (Hector) to complain, and says he wants his brother (Leonel) dead. Hector calls Leonel to him, and plunges his head into a barrel of water, holding him there, asking Marco if that's what he wants. Marco pummels Hector desperately until he releases Leonel, and asks him tearfully if he's all right. Hector tells them: 'Family is all'. Not only does this tell us why the Cousins, and the cartel, are such implacable enemies... it also horrifies us to see the innocence of two little boys who we know will become utterly evil and remorseless. But the entire scene would be incomprehensible without the dialogue, so the subtitles are essential.