I have the same issue on 3 of my 24 planets.  They are all in areas close to other races with the borders influenced by other races, but dont think the influence goes all the way to the planet itself.  Also, 2 of the 3 planets has ships from a somewhat unfriendly bordering race, although I am not at war with them.  Still, one plant is bordering the Alterans with I think the same Ideology as me and I havent seen unfriendly ships in the area.  I think there might be one border in the corner of this planets influce (far off) that is bordering a unfriendly race.

None of these planets started out with the -50% penalty to income with the "missing info" reason, but they all weree planets that were originally in the zones of control of other races, although none are now and one has hugely expanded. 

I was wandering if there was a tech I didn't notice that could be put on a starbase that might be within the area of influnce of my planet causing a negative to my income.  I do know it has nothing to do with the pentalty to raw producdtion from an extreme world.