This is a totally wrong perception of the universe we live in. The reality is that our knowledge of the universe is limited by the horizon of our perception.
In the years 1400 the existence of the american continents was not yet known because it simply was beyond the horizon of our planet exploration. These are huge continents with humans living on it that we ignored they existed but they existed. Today we know that dark matter [https://home.cern/about/physics/dark-matter] exist and that visible matter that is the only matter we studied until now accounts for only 5% of matter of the universe (current estimate). We currently don't know the nature and properties of dark matter. All we know is that it interacts with the gravitational force on visible matter and that is how we discovered its exitence. So, in theory, there is plenty of room in this unknown space that COULD support the existence of ghosts, spirits or whatever else.
We do have an extensive scientific model of the world in which we live, but it is still limited. What strikes me is that so few people seam aware of the horizon of our perception. I suspect it is due to our educative program that focus on transmitting things we know to students and forget to learn about the limit of our knowledge. This gives the false impression to young students that we nearly know everything and that there are only a few small black spots left.