They've also run things like the pioneer plaques (or maybe it was arecibo) past other scientists, who often have difficulty discerning the meaning behind them. If human scientists have difficulty discerning the meaning, I can only imagine what kind of difficulty aliens who speak in metaphor would have, let alone if they weren't linguists/scientists, which appear to be the case in the episode.

We evolved to hunt, and so it is suspected that as a result of that, we understand arrows to indicate direction. A species that hasn't evolved in such a way might not understand the meaning of arrows. Apply that same principle to language and you potentially have your problem.