A simple answer is that the planet is on an orbit with a high inclination relative to our line of sight. The other planets in the system may appear, from our perspective, to be in line with us and the star; we could then discover them through transits. This new planet, on the other hand, would never produce a transit as seen from our vantage point on Earth.
If the planet is habitable, it's likely low-mass and thus unlikely to produce strong radial velocity shifts in the motion of the star. This, combined with its orbit outside the plane of the system means that it is unlikely to gravitationally affect the other planets, making it hard to detect it indirectly (e.g. by transit timing variations).
Plus, as Luke suggested, the lack of transit observations would have made it difficult or impossible to perform spectroscopic observations of the planet's atmosphere. Non-transit methods wouldn't have revealed much about its habitability from an atmospheric perspective.