I would imagine its because they think other payments have been since made to Matuidi that MLS considers compensation and should be considered as part of the Designated Player determination.
At signing, Miami can say we are going to pay Matuidi $X and it looks reasonable. But perhaps since the last year, it may seem like Miami is paying for his housing and that should be considered comp, perhaps they made payments to his wife that were outside of his salary, etc.
There are probably many other potential scenarios than just the two above I noted, but that's what I'm guessing happened