Weird bug with colors/layers on Illustrator.

Hello.

I was working on an illustration and an unexpected bug has occured.

I'm using my Wacom Tablet to draw illustrations, and for unknown reasons the colors/layers in the artwork aren't overlapping each other.

The shading is suppose to be gray, but made it green so you can see where I'm trying to do it. The green is on the Shading layer, and the spoiler is on the Line Art. Colors are set to Adobe RGB (1998), opacity to 100%, and transparency settings to Normal. It's not even overlapping certain parts of the car too, which is weird.

Is there a solution to this? If so, let me know.