Moral Event Horizon: Although the Doctor has a very tragic and sympathetic reason for his atrocities it is this tragedy that blinds him to the fact that he is crossing the line by murdering several innocent characters throughout the film and even going so far as to threaten the life of the head doctor's young son just so he could teach him about loss.
Narm: The plague of rats. It's a pretty hard sell when the rats on screen look like they're just curiously crawling around instead of gnawing and scratching their victim. Likewise, the pilot himself just pushes them away or gropes clumsily for the one on his shoulder, never even trying to actually kill them: a task which really shouldn't be that hard for a man with leather gloves on.
Also the plague of bats. They're fruit bats, which while impressively large are probably not inclined to do much damage to a human. Plus they have cute widdle faces.◊
From this review: "Basically, the man in the bed has little to fear unless he is dressed as a plum or a juicy papaya (not, as we shall see later, that dressing up his victim as a mango or Bartlett pear should be considered beyond our villain, no)."
The last challenge, based on the Plague of the Death of the First-Born Son, requires the surgeon who failed to save Phibes' wife to cut out a key planted from behind his own son's heart that will allow him to deactivate a machine that will spray acid into his son's face if he takes too long getting the aforementioned key. This might as well be a prototype for the Saw films.
Not to mention the frog mask, which was exactly the kind of thing Jigsaw might have come up with for Mardi Gras.
Also, this is a film about a man with burned skin, supposedly dead, who takes revenge on those responsible, sometimes through their children. Hmmm.
And although the idea of the Poetic Serial Killer goes back way before this movie, it's fair to say that Se7en may have gotten some inspiration from Phibes' extreme creativity and use of religious motifs.
Squick: "And then he'll have a face... LIKE MINE!"