The games that 'fixed this issue' generally only add new content to the 'end' of the story lines of the previous release, thus they generally only need to check/validate the variable state of the last moment stored within the 'save' and don't need to concern themselves with the previous moments.
This game currently can add new content at any point along any of the story lines thus potentially changing the variable state of any of the moments stored within the 'save', also due to the fact you can generally progress each story line separately to each other and in an order of your choosing makes re-determining the resulting state of the final moment more difficult that it is in a standard 'add to the end' game.
While none of the above should be a Player's concern and it all comes under the heading of a technical issues that a Dev should 'just fix', it isn't always that simple to do so while the game is still being developed.
