If my passport has small puncture holes in it made by a staple from your agency when they returned it to me last year, will this cause a problem going through customs? Or should I come in and replace it and will the cost be my responsibility?

It depends where the small puncture is located. If is on the chip, custom might have a problem reading your personal information. I don't think you have to pay, it wasn't your fault.

I don't think the passport agency answers questions in Google. If You have a direct question you should call the number on the door, there is a picture with it. And I don't think small holes from staples are an issue but again I recommend you call and ask. And being a government agency, I'm pretty sure if the passport is damaged, you play for the replacement