Yes, a cross-check using the fuel quantities would show if there really was a discrepancy. The report doesn't say how the discrepancy was determined, so I'm only guessing it was an indication problem and it may have nothing to do with the FMS at all.
The FMS takes a snapshot of the fuel quantity at engine start and then uses fuel flow to calculate fuel remaining and fuel used. If the fuel flow information sent to the FMS was in error that might account for the discrepancy. Impossible to say without further information. Perhaps all will be revealed when the final report is issued, if ever.