As alligoat says, there are normally 3 points where water can get into a watch, caseback, stem seal/crown, and crystal.
After WP testing, you would have an idea of the area where it was leaking. Then you need to inspect that area to discover why.
Sometimes greasing or replacing a seal is all it takes, other times it is just not possible to seal the watch.
Each has its own characteristics. (Note that chronos have extra points of entry at the pushers, and these are sometimes VERY difficult to seal)
Crystals are another area where a seal is sometimes difficult to obtain. Most reps have push fit crystals with nylon seals, and if these get a nick they can prove very difficult. In a lot of cases, I replace the crystal with a larger one, discard the nylon seal, and glue the crystal into place. Not exactly how the manual says to go, however very effective, and time efficient.
Also check for porous cases; I have been seeing more and more, where air is leaking through pin holes in the case metal. Epoxy will make the case WP, but it will never be pressure proof!
Offshore