Layers in the middle of the frame???

Agree with Mylenium, hard to decipher what's wrong here from your screenshot, you've not show us the boundaries of the layer.

Most likely is that your artwork falls out of the artboard space in Illustrator, and you've then imported to AE as a composition without choosing "Retain Layer Size".  Try reimporting the AI file to AE, but select 

At the very least you could have selected a layer so we can see what its boundariess and layer anchor point are. Likewise, we would need soem info on how it's set up in AI in terms of artborad origin or possibly other things and what your import options were. Not ruling out AE being wrong, but it's more likely that you did not set up your AI file correctly or imported it using the wrong settings like layer size vs. comp size. At the very least check that part. Anything else wilol require more information as stated.

Mylenium