Actually, they are capable of rejecting boarding passes for the wrong flight.

Once in Orlando, I switched at the gate from a later flight to the flight that was boarding at the gate. The customer service agent accidently gave me back my original boarding pass (for the later flight). I only looked at the seat number and proceeded to board the flight. When I handed it to the agent putting the boarding passes through the machine, the machine "rejected" it because it was for a different flight.