Bob,

If I were your customer I would certainly confirm my board count before contacting you with a complaint. So, two things are possible (1) two boards were taken out before the count or, (2) only 48 boards were sent.

This then becomes a customer relations issue.  Sometimes extra boards are made.  If so, send him the two boards and keep the customer. If there are no extra boards, talk to the customer and see if the order can be closed short as it would be  a significant task to make only two boards.  Final solution, tell the customer that you shipped 50 boards and don't take further orders from that customer.

It's all up to you to decide if you want to go to the extra cost to keep the customer. 

Glen