So I clipped everything that was sticking out past the green box but there's a couple parts (I know exactly which ones) that just won't cooperate. I'm really bad at explaining things so i'll just post pictures step by step.
So I unclip the part I know is causing the problems. I clip the outlines and the circle without a problem (2nd image) but as soon as I clip that shading it doesn't want to stick like the rest (3rd image). I turned the blur off just to see if that did anything. It didn't.
Since its something that's happened multiple times for me I didn't think it was uncommon so that's why i'm here to see if anyone else has had this problem before and if they've ever found a way around it.