I've seen this often with Phobos and Deimos, very early in a game save, so I don't think number of objects in the solar system is necessarily the only factor, although I don't doubt that it's a factor! I think Blazer's point is good one too.
I've noticed that when your trajectory line crosses over something on the surface, that's sometimes when the surface object bugs out into space. That happened once with a big lunar base, and as I said it's happened many times on Phobos and Deimos.