The phrase cock-up seems to be given a different derivation with every new person that mentions it. I had always been told it was a military term to do with cocking a gun, but a quick search found this explanation on a couple of sites.

"A cock-up is a mistake. This is the same usage as a fuck-up or foul-up, although apparently its origins are from beer making. If the batch went bad, they turned the cock (ie tap, or faucet) up to drain the barrel."

I had never heard the theory that it came from a printing term before now.