According to BBC Sport, football's world governing body has written to the Premier League club "to seek clarification on the deal". It is believed to concern who was involved in the £89.3m transfer, and how much money was paid to them.
A United spokesman who spoke to BBC Sport said: "We do not comment on individual contracts. FIFA have had the documents since the transfer was concluded in August."
The 24-year-old French midfielder left England in 2012 for £1.5m only to return last year in a world record transfer deal worth 105m Euros.
Reports also suggest that the French star’s agent Mino Raiola might have earned a whopping £41 from the deal in question. In the deal, the Red devils also agreed to pay the Old Lady £4.5m in performance bonuses among other costs that include 5m Euros if the player pens a new contract.
Pogba first joined United in 2009 from French side Le Havre.