I didn't want to go on too long, but what you and others have noticed is the height of OBVIOUSNESS regarding what most developers do, THAT IS, the creativity and coherence of almost all of them leave much to be desired in terms of COHERENCE and CONCENTRATION OF FACTS throughout their plots. It's extremely RARE to see a game with a narrative that is coherent with the succession of events. There will always be these kinds of narrative holes that end up irritating players.
One game that ended up being abandoned and in which I saw coherence was "Watching My Wife." In that game, unusually, there was a succession of events that made the whole plot believable and well-structured, but this is rare to see in game plots.
And I'll go even further: in this game, from the very beginning, there were more narrative holes that many swallowed or turned a blind eye to, but they already hinted that illogical situations could arise later on, and that's exactly what happened with the girlfriend and the MC's father.