Lisa probably nailed it, but if not, make sure you go through the error check process.  There are boxes to check to tell the software how many months the taxpayer/spouse are HSA eligible, that may also be throwing you off.  If the only contributions are through payroll you only enter the code W on the W-2 Wks.  If there were additional contributions, only those "outside" contributions get entered on the 8889.

If they didn't contribute the full amount, this is when I explain how it works and suggest they might still want to make a prior-year "outside" contribution that we can deduct on the return.

Rick