David Beckham and other co-owners were cleared of any wrongdoing by the league, but managing owner Jorge Mas was fined £176,000 since he had an obligation to make sure rules were followed.
The investigation found Miami contravened team roster designation rules for Matuidi and Andres Reyes who 'should have occupied a designated player slot', MLS said in a statement.
The club was also found guilty of not disclosing agreements that led to the under-reporting of salaries for three other players, Leandro Gonzalez Pirez, Nicolas Figal and Julian Carranza.
Matuidi was signed from Juventus last August. Miami said it used targeted allocation funds to sign him, but the league ruled he should have been listed as a designated player.
Former Miami sporting director Paul McDonough, who parted ways with the team in December, was suspended by the league through the 2022 season.
The MLS also announced Miami's allocation dollars for 2022 and 2023 had been reduced by more than two million dollars.
The Sun reports that Beckham is 'furious' with McDonough for leaving the club in such a mess, while head coach Phil Neville is also dismayed with the hit to his transfer budget.
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