1. Literally, to form a hole in something by piercing it (with something else). Tommy, stop poking holes through your bread and eat it! She began absentmindedly poking a hole through her paper with her pen.

2. To identify or highlight some flaw in some plan, idea, argument, etc. Typically used in plural constructions. She quickly began poking holes through his theory. Before I offer up my own proposals, let me begin by poking a few holes through what opponent has suggested.