It appears to me that the initial error was that the Check-in acceptance limit was set at 16 when it should have been known that the maximum allowed with 1 crew member is 15 - it should have been very simple to block one seat and easier to handle a downgrading at Check-in.

Most operations departments can tell you what the crew configuration is hours before departure so it was proably an oversight noticed after close out of the flight .

Mistakes happen - but it is obvious in this case that the resolution of that mistake was not handled as effectively as it could have been