Why weren't the girls ever afraid of Mama during the five years in the cabin? Lily might have been too young to notice how different Mama was from normal human beings, but Victoria should have known better. Besides, aren't human beings conditioned to be afraid of anything that looks like a decomposing corpse that moves in a jerky, unnatural fashion? But then you realize: Mama has long flowing hair, a long flowing dress, and can fly. To a little girl's eyes, especially one without glasses, she can be mistaken for a fairy or an angel!
It also helps that Lily and Victoria were one and three years old, respectively. Three is still pretty young, and Mama was nothing but kind and protective of the girls until they were taken in by Lucas and Annabel. It's entirely possible that Victoria, like Lily, genuinely didn't see much wrong with Mama until they came across other humans.
The ending seems to suggest that Mama doesnt always look like a terrifying wraith. Its possible that when she cared for the girls alone, she just looked like a spectral human woman.
Alternatively, we are shown at the beginning that Victoria always took off her glasses when she went to meet Mama, because Mama told her to, as she didn't want to be seen as a monster by her. It explains why she angrily smashed them before the climax.
Why was Edith so fiercely protective and jealous towards her children? Her last act while alive was to leap (or fall) off a cliff to her death, and on the way down she smacked into a tree branch (which was probably what killed her, instead of the impact with the water.) But while she continued on to splash in the river, said child got stuck in the branch, and the authorities recovered only its body, not hers. So it's possible Edith never even realized her child was dead, and when she saw the girls, they literally replaced it in her mind and she believed they were hers. It was only when Annabel presented her with the baby's remains that Edith learned the truth, and might have been willing to accept this and move on had Lily not cried out for her.
Coupled with the fact that one little girl was named Lily - the same name that Edith's baby had - she might not have fully realized that she was even a different child...
When the two girls were first found, they were crawling on all fours and growling. This makes sense for Lily, who was young enough to have never learned to walk and talk before their parents' death, but Victoria should have been old enough to internalize those motions enough to remember them, even if separated from other people for years. But it makes sense if you consider who was their only role model for all that time: Mama/Edith walks (or moves, whatever you want to call it) on all fours and speaks in growls and shrieks; small children tend to copy the behaviour of the adults around them. It's possible they were trying to imitate Mama.
It seems at times convenient to the plot that Mama takes Why Don't You Just Shoot Him? lengths of time when attacking Annabel before finishing the job that enables Victoria to scream for her to stop, or that Mama simply (painfully) renders Lucas unconscious; compared to the quick and merciless ways she kills Jean and Dreyfuss. It's entirely possible that even before Victoria reminds Mama that she promised not to hurt Annabel, part of Mama is actually holding back when attacking Annabel or Lucas, because despite her Knight Templar Parent tendencies, another part of her damaged psyche knows Annabel or Lucas' deaths would upset the girls (Victoria especially) greatly after the girls have grown attached to their living guardians.
Lucas and Annabel may be safe from Mama, but they still have to deal with explaining to the authorities Aunt Jean's death and Lily's disappearance.
This is a universe where ghosts can and do exist, and Edith is not the only one; Jeff's spirit is shown to have a presence when he gives his brother a vision. Not only is he possibly still unaccounted for, but there's a strong possibility that there are even more of these dangerous entities lurking around.
There's no explanation in the film of how Mama found which baby was hers before killing the nun and stealing it. In the dream sequence, she just walks up to the first nun with a baby in her arms and takes it without even looking at it. Movie convenience says it's her baby, but it's also entirely possible that the baby she stole wasn't even hers, especially considering that she takes away another Lily who isn't her actual daughter in the end.
Or, for that matter, did she really even have a baby?
