You have to talk to Navient.  They would have passed the debt on to the Treasury Department Bureau of Fiscal Services, who perform the actual offset based on (in this case) Navient's instructions.  It may be that your wife was considered delinquent even though she was making payments (if she was past due for example) or it could be an error. At worst, the amount withheld should be credited to her account and reduce her future debt and payments.

Can they file a injured spouse to save some of the refund?

That would be another option yes of course.  But if they think no debt was delinquent and the offset was in error, the place to start is Navient.  If Navient can show that they were justified in requesting the offset (or the taxpayers decide not to fight Navient) then an injured spouse form would be the next step, assuming the original student loan debt was incurred before the marriage.