I meant it in the latter way: a metaphor can be useful as a pedagogical tool to introduce new ideas, and using the source of inspiration for this idea as the metaphor itself makes perfect sense, but unfortunately our brains seem to be prone to assign other properties of the metaphor that don't actually belong to the object of study.

I imagine this happens because we tend to conflate things that are similar, or maybe because it's not entirely clear which characteristics are being mapped in the metaphor?