Since you ordered assembly service, presumably they added tooling holes to the PCB to help facilitate some assembly step(s). It's a bit unusual because (usually) these holes are placed on the side-rails of the PCB panel, not on the actual design. But for prototype assembly, unless the size of your board is large or you order a lot of them, you don't get your own panel, so they need to treat each board individually during assembly.
Ed: I should note that they could have added side rails to your design, and still put your design in a shared panel...but maybe they've decided that those rails are just wasted space on the panel, and would rather put the holes on your design. Par for the course, I guess.