Every once in a while I will come across a comic that was printed without one of the staples. I can tell because there are no holes where the missing staple should be. I know that some printing flaws are excusable but that's a pretty big error. So, if the rest of the comic is in say VF+ how far should I knock it down?

According to the Overstreet Grading Guide, a missing staple that happens during the printing process is not considered a defect (other than a printing error).

For me, books with significant printing defects get a VF/NM designation.