So, employees were given a separate election for bonus pay; with the default being "no election -no withholding". As long as that was properly communicated, there wouldn't be a problem. The default could've easily been "no election - regular payroll withholding", but that's not relevant. As long as each employee was given ample opportunity to elect to defer, then there is no issue. It would even be nice if the regular salary reduction agreement for payroll advised that this election is for regular payroll only. So, without actually looking at all the facts, you cannot really conclude there is a problem. Until you ascertain there is a problem, there's really no need to vet a solution.
Good Luck!