What PART of the toe? Is it near the nail... Check for any hang nails, ingrown corners, etc. Also if you cut them too short it can hurt to have socks on.
Yes, he may have bumped it, stepped on something, or could even have a splinter in it...
Does his toe have a calous or harder area on the outer side of it? Check the WIDTH and not just the length of his shoes... Also, sometimes on shoes the place that the sole connects to the upper can seperate and have a ledge that will rub the sides.
If it continues to hurt in a week, then have a dr look at it...