Actually, there can be a wide number of spirits within one spiritomb. Many only contain one or a handful; others might contain ten, twenty, or more. There has even been a spiritomb on record that contained as many as 1000 spirits in it at once, although the keystone that held it together was barely holding itself together at that point. (The spiritomb unfortunately passed on shortly after its birth, but not without inflicting quite a bit of damage on the Sinnohan countryside.)
The “standard” 108 count is actually just a common number in folklore that just happened to coincide with the first spiritomb ever recorded. Mere coincidence, more or less.
The Pokédex According to Bill 