David Beckham's Inter Miami broke Major League Soccer (MLS) rules with the signing of France midfielder Blaise Matuidi from Juventus last year.
The MLS said Matuidi had been paid more than was allowed, effectively giving the team four "designated players" last season rather than the permitted three.
Designated players' wages do not count towards the MLS salary cap.
Known as the "Beckham rule", it was introduced when the ex-England captain joined Los Angeles Galaxy in 2007.
At that time, Beckham was given an option to purchase an expansion franchise, later becoming co-owner of Inter Miami, who played their first MLS game in March 2020.
In a statement, the MLS said World Cup winner Matuidi, 34, had been wrongly categorised as a "targeted allocation money" (TAM) player.
"Matuidi's compensation was above the compensation limit for a TAM player and he should have been classified as a designated player," the statement continued.
"As a result, Inter Miami CF violated the designated player limit as the team had three designated players in addition to Matuidi during 2020."
Any sanctions will be announced at a later date.
For the 2021 season, Matuidi has been registered as a designated player alongside Argentina striker Gonzalo Higuain and Mexico midfielder Rodolfo Pizarro.
As a result, Miami have had to buy out the contract of another designated player, Argentine midfielder Matias Pellegrini, who will join Fort Lauderdale - Miami's USL League One club - on loan and will not be eligible to play in the MLS this season.
Inter Miami are managed by former England women's manager and Beckham's ex-Manchester United team-mate Phil Neville.