Your employer needs to report the bonus as wages on form 941and include employment taxes. That means for a $200 bonus, about $30. Normally $15 would come from the employer and $15 from the employee. So at this point you can withhold an extra $15 (7.65%) from each employee on their last check of the year and say "oops", or you could be generous and pay the whole 15% so aren't taking money away. If you've already paid the last checks of the year you will either need to eat the employees' 7.65% share for 2016 and then make an adjustment in 2017 if you can.
Separately you were also supposed to withhold federal and state income tax according to the standard formula, but I don't see why you would need to pay that for the employees too. Just report the wages on the W-2. You made a withholding mistake but I don't think it's unforgiveable.
In the future, if you want the employee to net $200, ou would have to gross it up about 40% for state and federal taxes, whether you do that is up to you. (I just got a bonus, my employer added it to my wages and we all pay taxes. 60% is better than nothing.)
