Last week we helped out a client that had some deterioration at their front entry area. The entry has wood joists with basement underneath so we could see that water had penetrated the quarry tile floor. I was fairly sure there was no waterproof membrane under the mortar setting bed of the tile. Without a membrane water can penetrate the tile, the setting bed, and attack the wood substrate. Sure enough, when we pulled up the tile and setting bed we found significant deterioration of the rim joist, the ends of the floor joists and some of the plywood.
Fortunately this was an easy area to work in. We removed all decay, trimmed up the joists, installed new joists as needed, and topped it with new plywood. Then we installed a layer of ice and water guard that adheres to the plywood deck. On top of that the tile installer laid a rubber membrane. Both membranes were turned up at all the edges. The tile installer than laid some plastic reinforcing mesh and troweled on a setting bed. With everyting sloping properly this should take care of the water intrusion problem. But, if a good waterproof membrane would have been used initially there most likely would not have been a problem in the first place.