Neither the club nor the league would comment on the nature of the discrepancies, though it is understood that such issues are not uncommon.
Cardiff plan to use Sala's Premier League registration status to argue he was not their player when he died a month ago.
They have also written to Nantes seeking evidence that the French club had fully deregistered the Argentine prior to the Jan 21 crash.
As of yesterday, Nantes had yet to carry out threats issued earlier this month of legal action against Cardiff if the latter did not pay the first instalment of Sala's transfer fee.
Sala, whose body was recovered from plane wreckage two weeks ago, died from "head and trunk injuries". Pilot David Ibbotson is still missing but searches are set to be resumed for his body.
The Welsh club are continuing to build a negligence case against their French counterparts over the crash.More than one source said their case had been strengthened by an explosive interview given by Willie McKay to The Telegraph this week in which he confirmed that his agent son, Mark, had been contracted to work for Nantes.
The McKays, who helped broker Sala's deal, arranged his trips to Cardiff and back during transfer talks and the club plan to hold Nantes vicariously liable as a result if an official report finds that any flight regulations were breached on Jan 21. That could include rules governing safety equipment.
Relations between Cardiff and McKay Snr have deteriorated to such an extent that the club have written to him warning that they reserve the right to deny him entry to their ground.
Nantes and the McKays have also found themselves at the centre of unrelated tax wrangles. Inspectors searched club premises at Nantes on Tuesday as an evasion investigation was launched by the National Public Prosecutor against the club's president, Waldemar Kita. Nantes were not immediately able to comment.
Meanwhile, a High Court hearing in London heard how Mercato Sports Ltd, a business registered in the names of Mark McKay and Willie McKay's wife, had cleared a tax debt in a last-gasp bid to fend of an HM Revenue and Customs winding up order.
The McKay family business, Mercato Sports, was yesterday mentioned briefly at the Insolvency and Bankruptcy Court at the Rolls Building in central London. A barrister for HMRC told the court: "The debt has been paid. The petition is dismissed with costs."
- The Daily Telegraph