After a thorough search and no solution, I decided to ask here.
So this happens:
I create some shapes in illustrator, I release everything to separate layers, save and go into after effects.
I import the ai file as a composition with retained layer sizes. Up to here everything seems to be perfect.
I need to animate some of the shapes, though, so I convert the layers to shapes.
Some of the layers create additional paths in groups which did not exist in AI. The additional paths are always as big as the entire composition. So, if the top layer creates such an additional path I can't directly select anything beneath it. The layer contains both the original shape I created plus the additional rectangular shape which encompasses the entire composition size.
I can, of course, go and manually delete each additional group in all the layers that contain it, but this seems weird to me. I must be missing something here.
Before the conversion to vector I can freely select each shape, as the size is retained. After I convert, I can no longer do it. I have to search for the layer I need manually in the layer stack.