Can an employer make an employee pay for a shortage?

IF it had been one of the terms of employment, that employees had to make up for shortfalls of various kinds, then yes--it would be legal. But it has to have been an actual employment policy of which employees were aware, so that they could have chose to not work there if they didn't like the term. (So that by continuing to work there, they could said to have agreed to the term.)

The company cannot suddenly or retroactively apply a term or requirement like this to you.

However, be aware that it would be legal for your company to fire you if they choose--employers may generally fire someone for any reason, at any time. So if you refuse, they can't take the money from you, but they could terminate you.

This is a good news/bad news scenario.  The good news is that your employer cannot take the money out of your check unless you agree or if the terms of your employment say that they can.  For example, if there was a stated company policy, or an employment/union contract provided for this, or you were being singled out and discriminated against ( based on race, age, religion, sex, disability or any other protected class). 

However, the bad news is, that your boss could fire you for the mistake or give you the choice of repaying the money or being fired (although legally you'd have the right to not pay).  If fact, as an "at will" employee, your employer could fire you for no reason at all.