My take on this movie (obviously spoilers abound)

So, this probably won't be seen but I thought I might as well contribute a theory having just watched this movie myself. (Warning, very long reasoning)

Having seen some of the "Daisy is autistic and the people have created events from fear" theories, I do think that is probably the case. The fear they have developed of Daisy through the folk tales of changelings and fairies has manifested itself through stress.

As viewers we are led to believe that Daisy is a changeling by the timing of certain shots (e.g. the social worker's card vs. her death, whenever Daisy narrows her eyes or looks particularly creepy when something bad happens, etc.)

I like the fairy changeling theory as it then explains away a lot in the film that the autism idea doesn't; the boils on Sean Cryan's face after Daisy spits on him (though this could have been caused by the next scene where he scrubs frantically at his face, possibly catching the skin and causing it to go septic or something), the perfect timing of the car and the card (coincidence?), the three children getting meningitis at the same time (coincidence again? Daisy has a naturally higher immune system?).

Now, it's stated early in the film that Martha previously had a baby, Chloe, who died. And then Martha develops a motherly attachment to this damaged child whose entire family has died. Some folklore states that a changeling is a sick fairy baby that is exchanged for a human baby so that the sick baby can be nurtured back to health. What is the Chloe that died was a changeling, and Daisy can detect that? It is also stated that Daisy tried to kill her little brother (succeeding the second time round) by smothering him when he was younger. This makes some sort of sense because then Daisy's "real" parents would be forced to care for her and only her as there would be no second child to look after.

Also, note the perfect timing of Daisy's parents death and Daisy becoming integrated into Martha and Thomas' lives. Daisy has been kept in a shed and her parents had planned to burn her because they believed she was a changeling. Martha was the only one being nice to Daisy, and she was also the added bonus of being pregnant (hush, I'll get to this later). So Daisy begins to develop this attachment to Martha, but her parents are still alive. So, what does she do? Somehow reverses the fate they'd planned for her onto them. Quite poetic, actually. So they die in the fire instead of her. And who is the first person to Daisy's defence? Martha.

Changeling's are fairy children that were swapped with human children, yes? If the "Daisy is a changeling" theory is true, and Daisy knows she is a fairy, then theoretically it makes sense that Daisy would also try to take human babies in order for her fairy kin to place their own children in the babies place. This is where the whole thing about Daisy picking Martha because she's pregnant comes in. In my mind Daisy can sense that the child is healthy and is planning to turn it into a changeling. But how can she get close enough to the healthy child in order to swap it? This is when she decides to kill her family and ruin any plans to take her away from Martha and Thomas. If you're asking why she didn't go to Kat, remember how even before Martha and Thomas arrived the whole town still treated her with suspicion. Yeah, she was hated long before the movie.

Then comes that last scene, where Martha begins to bleed when Daisy places her hands on her belly. I think what had happened, was Martha had either an ectopic pregnancy and was miscarrying but Daisy was trying to save the child, or something else had gone wrong that meant Martha was miscarrying and Daisy was trying to save/kill the baby. The reason I say this is because surely the only time you'd bleed whilst pregnant is because you are having a miscarriage? I swear when your water breaks, that is what it is, water/the liquid the baby was bathing in... Martha miscarrying also explains the pain that she was feeling when Daisy placed her hands on her stomach.
Now for the reason Daisy is trying to save/kill the baby:

Save: For the entire movie Daisy has made sure she almost always stays with Martha. The entire movie. If this was because she planned to change the baby into a changeling then a miscarriage would most certainly undo all her hard work. So she feels Martha miscarrying and has to choose whether to save Martha or the baby. In this case she chooses the baby. But when Thomas finds them and takes the baby away Daisy realises that she will never get the baby again, so rather than allow Thomas to take the baby she uses the baby doll to act as a "voodoo doll" of sorts and suffocate the baby in Thomas' arms. Like crib death, the baby in Thomas' arms will just stop breathing.
OR the child in the cot had already been switched when Thomas took it away. And Daisy was making sure the human baby was being killed when she put the blanket over the baby doll's head. Although for the majority of the movie that was foreshadowing the revelation that she'd tried to smother her brother when they were younger.

Kill: She could have been trying to kill the baby by force because there was still the chance for Martha to get pregnant again. But she failed killing the baby the first time round (and also accidentally kills Martha in the process), so when Thomas takes the baby away she has the perfect time to kill the baby without being rationally instigated for it. Yes the town is steeped in folklore but "magic" wouldn't actually hold up in a court of law.

She tried to smother her brother and then drowned him. What if, in the last scene she had switched Martha's baby for a changeling, but Martha's real baby was drowned in the bath tub and Thomas hadn't seen it? Then the act of covering the baby doll's head with the blanket could be symbolic of Daisy making sure the baby in the bathtub drowned or suffocated, seeing as the new baby is her new younger brother/sibling of sorts.
Added to this is the fact that most children taking by the fairies were un-baptised baby boys.


That's just my take on it.