It happens quite frequently in my experience, particularly when you try to sell your first bundle of Sis for example. One of the shopkeeper sound effects indicates that he's restocking more money, but I don't remember which one.
My experience is that it seems to be strongly level dependent. Past level ~20 or so, I've never had this happen.
If there's items that you want to buy, you can buy some stuff to free up some of his money, then sell other stuff to get it back. If there's nothing you want, you'll have to wait...
Hoping to win with every class, doomed. Archer, Barbarian, Bard, Beastfighter, Druid, Elementalist, Farmer, Fighter, Monk, and ULE Priest down.