I have had several not in the boxes, you can put some golf balls in there it will encourage them to use the boxes... or don't let them out of the coop for a couple hours, see if they lay inside the boxes.
It happens from time to time until they get used to laying in the boxes. If you haven't already, make the boxes dark and safe feeling for them and soft and comfy with shavings or straw. They'll get the hang if it soon enough.
my first egg was in the box it had alot of straw in it but me younger birds kicked it all out and i have had golf balls in the boxes for like 2 months
