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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