It's not obvious when this "breach" took place, either during the formal (pre-covid) franchise contract period, or during the more recent EMA/ERMA contract periods.
I suspect it's the former, as the DfT takes all the revenue for a management fee in the present situation, with less scope for fiddling the books.
Really the action amounts to removing Govia from the expectation of a direct award for the South Eastern service contract.
It does turn the spotlight on other Govia matters, though (ie GTR), if they allowed irregularities like this to happen at SE on their watch.
Keolis are in there too as part of Govia, but I imagine they wouldn't be involved in day-to-day operation of the franchise.
Is Michael Holden busy at the moment?
It could be déjà vu, all over again...
Going right back, apart from DfT intervention over the two South Eastern issues, the franchising process found irregularities at the LT&S (now c2c) BR operation which delayed the initial franchise award.