I guess that's the downside of the:
1.Sandbox aspect - since you are free to enjoy the game and what it has to offer even if the story suffers, problem that can be solved (
like we see when Maria goes to think about her feelings for you) but it takes time and leads to the second problem
2.Development cycle - most of the problems with the inconsistencies between story and gameplay can be solved by changing certain lines of dialogue and locking events/interactions with a character for a time but that would take development time and some people won't care to go back to an old event that was reworked to remove such inconsistencies
Now when it comes to the 2 examples you gave the simple answer is: this is an adult game so logic has to be bent
The more involved, story wise, answer is: