Hi, here’s a solution that worked for me. I’ve been having this same problem as you and I find it annoying because it doesn’t let you animate your shapes in their own area.
The solution I found, is to have every element expanded, do not use strokes, transparency or blending modes in any object, be sure to have everything in a flat way. I tried many many things before to figure out what was happening but in the end I came out with this solution which just worked for me a couple of days ago. The other way to do it is by deleting that “Group 1” that AE creates but that wouldn’t be an option if you haven many shapes.
Anyway, I hope this works for you as well, good luck!