I have a path in Illustrator that I paste into a shape layer in AE.
The path in Illustrator has a fill color with holes in it. When I paste it in AE, it's the the holes that take the fill color, and the shape around them becomes transparent, instead of the other way round
Check the order in which the paths are placed in AE and naturally you may have to apply a Merge Paths operator to restore the logic of operations. AE's shape layers have no native awareness of these things.