I am not able to duplicate this issue on my Mac running the latest version of Premiere and AE. My AE comps duplicate just like your footage.
Are you on Mac or PC? What versions of CC?
If you drag the AE Comp from your project bin multiple times instead of alt-dragging on the timeline, does that create multiple copies in your bin?
If you click the comp in your time line, Copy it, move your timeline indicator and Paste, does that create multiple copies in your bin?