+1
Bonus when she insists that her boyfriend still has to use condoms.
Nothing of what you listed is a plot hole.
Part of your list sounds like you just don't like NTR. Which is fine but weird as criticism of an NTR story.
8), 9) and 10) are definitely a common problem, often paired with too fast pacing. Stories that do this right are unicorns. Edit: then again those points also apply to roughly 99% of all other nsfw stories.
Not sure how much of it is already known but I encountered a couple (mostly minor) bugs:
The game's surprisingly fun, thanks for making it. Also is there a donation button I'm not seeing considering the description mentions it?
Edit: also you can always peg the son by entering the room without normal clothes, even with 0 energy. The energy will go into the negative numbers.
Edit 2: after giving the son a magazine entering his room at night doesn't work anymore it seems.