Problem
Natural stones by definition are not regulated in terms of porosity and movement.
Sandstone and limestone will be porous, granite and marble will be quite dense, slate could warp.
With uncalibrated tiles (i.e. tiles that do not have a constant thickness), such as some slate and terracotta, it is difficult to achieve a flat and level finish on the surface of the tiles.
They also require an adhesive that can be used at a bed thickness sufficient to cancel out the variation in the tiles.
Some light-coloured limestone/marble tiles are translucent resulting in the adhesive being seen through the tile. If a grey adhesive is used this can make the tile appear darker in shade once installed.
A spot-fixed method of fixing should not be used by tilers as it can result in shadows being seen from the tile face where the adhesive is in contact and also increases the likelihood of pointload breakage.
Grout can scratch soft glazed tiles (such as hand-made tiles) and the surface of soft stone (such as marble).
Solution
Use adhesives and grouts specifically designed for natural
These fixing materials include thick bed, rapid or standard-setting flexible adhesives in grey and white, complimented by flexible wide joint and flexible fine-textured grout. There is also a highly flexible, stonecompatible silicone sealant for movement joints.
