A dark 'stain' that appears without reason is more than likely to be mould. This can be treated.
A stain that is a genuine stain from food or oils or drinks is another issue. We need to remember that terracotta is a natural and a porous product. It will absorb liquids and oils and these will stain the tile. A buildup of these can actually be part of the character and charm of terracotta. It is a natural aging process or 'patina.'
Efflorescence will cause a white powder or stain to appear on the tile. This is a layer of soluble salts that is left behind after water has migrated through the body of the tile.
Mould is a growth that can be found on unglazed tiles or grout where there is dampness and the conditions are right.
Staining will always be a factor to be taken into account when purchasing an unglazed tile, as this sort of product is porous and susceptible to staining.
Mould will need to be cleaned off using Heavy Duty Tile and Grout Cleaner. Once the tile is clean and well rinsed, it will help to use a penetrating sealer like Sealers Choice. It needs to be appreciated, however, that mould will probably keep reappearing in damp conditions. Penetrating sealers like Sealers Choice are not permanent protection for unglazed tiles in outside situations.
Note: Sealers Choice will not change the colour or surface of unglazed terracotta tiles.