Not sure if this has been said before - I checked the OP but didn't see any list of known bugs.
I've seen multiple instances of planets showing up as black dots against the sun - as if they were transiting it - even though they are behind it. For example, Jool should never transit the sun from my point of view from Kerbin, but it shows up as a black dot against the Sun when it passes behind the sun. Seems like a occlusion problem, but I'm not sure. I can drop a log/screenshot/whatever you need to bugfix.