If by "undertone" you mean implication, this is a subject that can have more to do with situation or cultural tendencies than language, oftentimes. I'm sure that, in your language, you have often observed people talking about one thing but obviously meaning something else. I don't know of any specific trick to recognizing such things other than life experience.
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While I wouldn't necessarily disagree with what Jura says, she seems to be talking about "tone", "undertone" and "tone of voice" (note: the first two are not always "tone" in the sense of sound) as if they were pretty much all the same thing. Perhaps, if you gave more information, such as a specific instance in which you were confused, this question could be answered more precisely.