Can contracts programmed in bitcoins be used to scam merchants?
Simple answer, no. What you're most likely talking about are interesting ways to use script to pay to a m-of-n multisig, for example. Generally, when you get paid in bitcoin, you, as the merchant, get to choose where the customer sends the bitcoin. This can be 2-of-3 multisig, which would mean 2 of the 3 people you choose have to agree in order to move the bitcoins or something much more complicated. But the address that the user sends the money to is entirely up to you, the merchant.

A more complex answer is maybe. It is possible if you're using some complicated escrow system that a customer may be able to hold the bitcoins hostage, but that's not something you have to worry about unless you specifically choose that sort of payment system. The vast majority of merchants that take bitcoin don't do business this way, they simply take payment into a standard bitcoin address.