Don’t forget the possibility that the rock was already in your shoe but your movement wiggled it out of place and into a spot that you could now feel it with your foot.
You ever ride a bike through a mud puddle and have it spray a bunch of mud up the back of your shirt? Imagine your shoe is like the bike tire. As you walk small stones or debris get kicked up in the air behind you and occasionally one of those might fall down around your ankle and work its way down into your shoe. It’s not really arching, it’s just going up in the air and then falling down, but your shoe happens to be in the landing area instead of the ground.
As an experiment: if you shuffle your feet along instead of walking like a normal human, I bet you’ll experience fewer rocks in your shoe.
Or, if none of that sounds plausible to you. Then the answer is magic
You partially answered your own question. Humans are pretty big compared to rocks. Any given step with some set of angles relative to the rock will kick up a pebble here and there. The tongue of the shoe (part right over the ankle on front) is also not perfectly attached to the rest of the shoe in many cases. So pebbles can also go from the top of your shoe and then wriggle in
These are just the two mechanisms I can think of off the top of my head.
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