Some flaws...

[veeria]

I thought it was made quite clear in the game that it was indeed Frisk crawling in the tunnels. I don't remember the part exactly but the readables hinted to it very strongly. Also the noises he made and the fact he came out only in the darkness were a dead giveaway.

As for Amabel, I always thought she was way creepier than Clarence. She seemed to have completely snapped and was not living in the reality of the situation. She was always overly calm and certain that everything was gonna be alright when she should actually have been hysterical. As soon as Philip got in the same room with her she totally flipped and went homicidal is what I always thought. Her craziness was so subtle that I honestly don't know if it was intended because some people probably didn't experience it the same way I did. Dunno if I'm giving the devs too much credit but it really worked for me like that.

Being hysterical for a full year would be pretty devastating. I interpreted her nervous ramblings as (barely)coping with stress and all that. Besides, I don't think everyone is the kind to react to bad situations with hysteria.

As for Frisk in the tunnels, well the notes outright said he made a habit of avoiding light and digging holes in the walls. Holes of the exact same size and shape as the one in the storage.