they get stuck when the car's various panels flex. As they relax, they capture this debris. Many of them wouldn't even fit in some of the gaps otherwise.

 

Use a polyurethane trim removal tool to gently open the gap first, then use wooden coffee stirrer to push the pebbles out. If you try to push pebbles out without opening the gap, they are likely being held by the body work and pushing them can cause the pebbles to damage the paint.