These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Paranoia Fuel: Flowey knows about your instruction manual. Flowey knows what you did... and he'll leave a message to let you know it. Flowey also knows when you save scum and when you stick your nose where it isn't wanted (the website source code). You can't hide. Hee hee...
In-game, try to walk a screen or so into a room (such as the first save room), then walk back to its entrance. You might see a spying Flowey quickly running out of the room.
Even more so than that, killing her, then going back to save her. Flowey knows what you did.
Enjoy being an aloof completionist and seeing every possible route? Well, then, if you save Toriel on your first runthrough, you'll have to go back and kill her to see what happens, won't you? After all, it's not like it's something you'd actually do, you just want to see everything. Nice try. Once again, Flowey knows what you did.