Wales interim coach Rob Howley questioned the integrity of the game after watching his team go down to defeat following a converted try in the 100th minute of the clash at the Stade de France.
The visitors were upset Les Bleus changed their tight-head prop 11 minutes into the 20 minutes of added-on time during a series of nine scrums.
France's team doctor said Uini Atonio needed to go off for a head injury assessment, meaning Rabah Slimani came back on for the final few minutes.
Wales have also alleged wing George North was bitten during the build-up to France's match-winning try although the incident was checked at the time by the television match official Peter Fitzgibbon, who could find no clear evidence to support the claim.
Six Nations Rugby have now said they plan to look into both incidents, adding they are "aware of concerns" regarding the head injury assessment protocol.
Speaking after the game on Saturday, Howley said: "In terms of the process, I think we have reason to complain.
"You can hear referee Wayne Barnes ask him if he is OK. He said he had a sore back but that he was OK. And then the doctor comes on and he goes off.
"I've no issues about the result, it's just about the process."