I noticed that this message is left on screen.
There is also this which I wrote before but for some reason the comment could not get added, so I post it now:
(those are for chapter 2 of Stalker (is it on purpose that chapter is named stalker when he doesn't have mask and Sebastian when he does?))
I have a problem with getting to some of the endings (may be my fault though).
1. This part of the guide says that I need to accumulate different acts of submission and gain Sebastian's trust
but what does it mean? If it is related to the amount of points for heart then after Sebastian asks if I love him -> Yes and then letting the timer run out for cuddles I have 95 points there but still get 'There is no escape' ending:

On a side note I noticed that in case of skipping or rolling back sometimes icons are left on screen as above.
I manged to get out of the basemant but my sanity was very low, and one of this endings requires >=35 sanity
Also isn't it the other way around? I had sanity at 0 and didn't get to chose to go to the officer (there was no choice). I'm not sure where the choice should be so I just add screen of end with my sanity:

2. When I chose Basement here it ends the same as when timer runs out (A thousands words)
4. There is if/else but no information on what it is about (was this ment to be like this?)
also here:

was there supposed to be value for sanity here?
5. I also can't get here to the Escape branch:

which punishment does this mean? I don't get here after last one. I also think that maybe getting paper clip may be bugged somehow. I managed to get it when I didn't do anything to get it. I have this:
and the next one is this:

So I don't really know where it came from.
MAJOR SPOILERS AHEAD
Maybe I can answer some questions for you, so you can advance in the game even with those bugs :)
1. I don't think getting upstairs is related to love points. You just need to submit to most of Sebastian's request iirc, because you can still have high love points without having his trust (thinking about the pain slut achievement lol). Also, you need to keep a certain amount of sanity or you'll get the "You don't want to leave" ending when Seb allows you to go upstairs. I've also noticed that on some routes the <= and >= symbol are sometimes inverted. Even the sanity value can be wrong sometimes. On Daniela's route, for the ending "Sorry" and "Daniela's Pet", it says sanity > 10, but it should be sanity < 10, but even then it's possible to get the endings with a sanity of 20. So yeah, gotta keep that in mind sometimes I guess ^^"
2. I think it's because your sanity is too low, so you don't want to go back to the basement. You need to make sure it's at >= 30. In my playthrough, when I got upstairs, I decided to go through the basement, but it lowered my sanity a lot and, just like you, I didn't want to go to the basement when I had to escape, which made the timer run out. To avoid that, when you get upstairs, you need to make Sebastian suspicisous. To do so, stay silent when Seb asks you about the food he made and say "No stop" in the bathroom or before going in. Then, when Seb asks you if you love him, just say "Yes" before the timer runs out. Of course, you need to make sure you have enough sanity before going upstairs and before going through the basement to unlock the cupboard.
4. It's about the love meter for the Beg route. If you have enough love points, Seb will stop :). But yeah, it should be shown in the tree imo.
For the "Deal with it" ending, you need to have sanity higher than something I guess. I cannot precisely remember how high it was in my playthrough tho :( Maybe like 30-35? I can recommend to not go through the basement and to make Seb suspicious, then say that you love him. Now, if your sanity is loooow, you'll get "Happily ever after". Once again, it should be show in the tree lol.
5. Punishment = any punishment I think (the candle, the clowns, the claustrophobia, the arachnophobia).
I have the same problem with the screwdriver and the paper clip! Even if I get the screwdriver AND my sanity is >= 60 (i tried lower, just in case the sign was inverted), I can never get "Look for escape" with "Nothing" and "Call for help". I've tried not submitting to Seb and I've tried submitting to him, just in case, but still no "Look for escape".
Plus, just like you, I get a message at some point that I got the paper clip, which I didn't, and I still get the "There is no escape" ending haha.
Hope that could help you a little bit!