The three holdovers were over the original price threshold for being FA, but under the new one.
When the first FA were released, they remained on their newly botted team while on the TL. They were also locked from being replaced. There were a few cases where a new owner would be assigned one of these bot teams, and would get 18 new players, and have holdover players who were already on the TL (the new owner could actually bid to try to keep "his" players). In one instance, the transfer appeared to not have gone through, and the new owner got the holdovers. In other cases, it appeared that a new owner may have got the money.
To fix these problems, BB moved the FA off of the bot teams at the same time they were placed on the TL. If a new owner was assigned, the players would already be off the roster.
Then BB increased the salary threshold. The few players over the new threshold continue to be removed from the rosters. But it appears that the players were over the original threshold are still being locked on the roster, but since they aren't being sold they actually remain on the team.