You probably have some planets that are in the wrong stars, or you have solar systems stacked on top of each other, or something weird like that. When you create new planets, it makes them in the star system of the solar system you clicked in. Even if you move it to where another Star is.
Likewise, Solar Systems will always be on significantly different points on the Z-axis, so having star systems overlap each other will always have somewhat unpredictable results.