I've noticed various 'fridge logic' problems with Heaven Sent, but I don't think it alters my fondness for it (I similarly like Inside the Spaceship even though it makes no sense).

Hell Bent was also good, although as you indicate it felt a bit like one for the fans, from Rassilon and Gallifrey to gender-bending Time Lords and the traditional new Who tears before bedtime, although I think on the whole I'm glad Clara survived, albeit as a zombie. I think overall it was a strong end to a strong season, what might be the best new Who season, although as I said to parrot_knight, I would distinguish 'best' from 'favourite' - it was too dark to really be my favourite season.