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They have spent years together at this point. Linguistics is just pattern analysis so some humans ended up cracking it and understanding; it doesn't hurt that they could grab one of them, put them in a cell, take an object, and play an audio clip to get confirmation, or something. Beyond that, it would take some time, but you can understand a language and speak your own language even with our languages we have here; if both can recognize and understand what was said, it doesn't matter that they weren't both speaking the same language. I and my girlfriend do this sometimes where I'll say something in english and she'll respond in spanish, for example.
They even have an interpreter at one point in the film translating from the prawn's language to english
