Spoiler The Door

Yep, felt like a plot hole; especially weird that the characters don't question it. Only answer we could think of is:

Before waking up and finding the kid asleep. Travis sleep walks to:

Sneak into parents room and grab key (is it on the wall at night or still on his neck?).
Open doors to look for dog
Returns key
Returns to bed

In this scenario Travis ends up infecting the kid.

I like the theory that Travis sleep walks! Especially with the dream sequences blurring the line between what's real and what's imagined.

My theory was that there's some kind of monster on the very fringe of the movie. Maybe something that people turn into after they get infected? That's why they kill the infected and burn the bodies, why they don't like to go out at night. You see a brief glimpse of some kind of humanoid something sitting in the woods during the driving scene. My guess is, that's the monster. The dog eventually goes after it and gets himself killed. It brings the dog back, opening both doors. The little boy gets into that room, and the infection begins.

That's just what I thought in the theatre. It's been awesome reading other people's interpretations.

Maybe the one of the parents opened the door? Maybe they were infected and have no recollection?

Travis claimed the doors were open when he came down - he told them that. It then became "who opened the doors". Travis then tells them that he found the little boy.

Since Travis' Dad has the only key then either Travis sleepwalking is an option, or the Dad opened it.

The little boy couldn't of done it and his parents wouldn't have the key.

I have two theories:
1) The dad opened the door to create a rift between his family and Wil's. He really didn't trust other people, and seemed to want the family to keep to themselves. He mentions to Travis that he should only trust his family. Plus, there were so many camera shots of Travis looking at Kim, or Travis bonding with Wil over chopping wood, or Sara bonding with Kim while decontaiminating the water, and Travis's late night with Kim. Maybe the dad thought he could blame Stanely getting on the new people.
2) Travis opened the door while he was sleepwalking. We do see him out in the woods desperately searching for Stanely. It's possible he can't remember he was sleepwalking, my sister does, and she doesn't remember sleepwalking. So, maybe Travis rescued Stanely from whatever creature was after them and brought the dog home. Andrew couldn't remember why or how he woke up in Bud's room. Maybe sleepwalking is a side effect of the illness or something.

I'm really surprised that there's people out there wanting answers to any questions they may have after watching this movie.

When a movie is as bad as this one it's best to just put it down to poor script writing and then move on, don't waste any more time rattling your brain for explanations.

I think there are deliberately weird parts to this movie/story, such as the dog running off barking and then suddenly not, and then coming back. 'It Comes At Night', perhaps there is an undertone supernatural element to this film not easily picked up on. Is the disease just a disease or is it more? Is it black magic, a curse, witchery etc. I think that's actually the plausible answer, something kinda spooky going on.
Furthermore there are moments when we see Andrew having nightmares about the sickness, going out into the woods, being horrified at what he sees, his drawings. I think if you look hard enough this is not a regular run of the mill apocalyptic WWZ/Contagion style flick, I think it has a subtle but deliberate 'supernatural horror' twist to it.