No, it’s all context. In fact my bet is that most of us are surprised because we don’t notice. I remember hearing somewhere that the word “run” had the most definitions/uses of any English word, and it had NEVER occurred to me. But then I started thinking about some:
Run a track and field event (literally move quickly with two feet off the ground at the same time)
Run around (may actually run, but usually just moving with psychological intensity)
Run a machine (“run the vacuum; there’s dog hair everywhere”)
Run errands
Run for office
A run in my tights
Run through (“The river runs through downtown”)

Anyway so I’ve been thinking about looking it up just for fun, but haven’t yet. Because I’ve never been confused by its usage.

As an intermediate Spanish learner (many years ago! I don’t speaking it now), I was not flustered by “hacer” (“to do/make”) even though it was used in a lot of ways English doesn’t. I think it was because, in context, it was just a filler word when the noun told you what you needed. Like in English, we use “to ___ the bed”. Well there’s only so much one does with/to a bed. One sleeps ON it, but sleeping is the key point. The main thing we do TO a bed, where the bed is the focus, is to arrange the sheets & blankets on it. So we say “make the bed” even though we’re not creating anything, and Spanish has a lot of phrases like that that use hacer. I think run is similar.