My guess is this dot got added to the team manually by Support after the dot was 1000d old. 1000d+ dots can re-sign contracts with an existing team, but can't be sent new contracts through the system if they are/become FAs. I assume when the game was coded, no one foresaw 'retirement teams' with dots 1000d+ would be a thing, so '999' was used as the 'maximum' value. However, Owners/Agents can request a 1000d+ dot be added manually to a team. When Support manually adds, the contract is "frozen" (doesn't expire) until/unless a new contract is offered by the team. At least this is how it's worked in the past. On my retirement team (Elysium Immortals), I always send out new contracts, so you don't usually see this "quirk".
Side note, we've got room for 1 more 480d+ dot on Elysium Immortals this season if anyone's interested!