Why does my stable get dirty when there's no chocobo in it?

Seems curious.

Unless there's a dirty homeless lalafell living in my stable at night time that I don't know about.

If you leave an empty room unattended it will still gather dust, even more so with something that is outside ^.^

The stable is outside. In addition to the homeless, there are pigeons, rodents, other vermin. Not to mention the neighbor's chocobos sneaking over to see if any treats got left behind.

you mean to tell me thats not the miqote litter box? :O

Plus there's simply the wind. two out of the three housing areas have sand that would blow in, and the third has soil.