Though I am not entirely sure to what you are referring, I’ll try to answer. We cannot see some objects, such as rogue planets and dim stars, since they don’t emit much light. We can, however, see the effect that these objects have on surrounding objects that are visible. The objects seem to behave “oddly” in our models which do not include the “missing” object. We might see a distant star with a wobble, which is most easily explained by it being a binary star system with a brown dwarf. This is how we find “exo-planets”, planets outside our solar system. These objects are far too distant to be viewed directly, but we can see the wobbly of the star and the occasional dimming as the exo-planet moves around it. This is also the technique we would use to find blackholes, which don’t emit light, but exert a huge gravitational force in the surrounding area.
The take-away should be that we can see the effects that these unseen objects create in the surrounding region.