Problems creating shapes from vector layer

I have a logo in Illustrator I'm trying to import into After Effects. This logo constitutes 3 shapes: 2 squares 1 circle. If you look at the top right, the layers are three in numbers representing the shape layers.

 While I import it into After Effects as Footage so I can create shapes from vector, it does something interestingly opposite after the conversion. 

 It creates the Pathfinder effect(Divide) or Boolean effect such that where the shapes overlap or come in contact, it creates an extra layer. If you look at the bottom left to count the groups, they are now 4 in numbers.

This hasn't happened before. I don't know why it's happening now. How can I fix this?