1. Literally, to form a hole in something by piercing it (with something else). Tommy, stop poking holes in your bread and eat it! She began absentmindedly poking a hole in 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 in his theory. Before I offer up my own proposals, let me begin by poking a few holes in what opponent has suggested.