Plausible reason not to notice a planet
Imagine a generation ship heading for a distant star. Humanity had means to observe that star up to a point, that it is 99.9% sure the star has a colonizable Earth-like planet (with water and atmosphere). So sure enough to send the ship in the first place.
On the way to this star the ship needs to refuel its fusion engine and passes some other stars that have Jupiter like planets. It is going to collect the fuel there to continue its journey. When it approaches this intermidiate star system, it discovers an Earth-like planet in the colonizable area.
Now the question. Is there a plausible explanation as to why this Earth-like planet in the middle-station star system wasn't discovered before (from Earth, when planning the expedition)? Which [future] technology could allow on one hand to predict the conditions on a far away planet and simultaneously completely overlook another planet?
I was thinking that e.g. the Earth-planet is kind of always behind the Jupiter-planet when observed from Earth, so always covered by it. Are such trajectories of two planets even possible?
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1 answer
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.
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