How did Alex get into the house each time?
The first time it would have been during the day. She does the bunny boiler thing. How did she break in? How did she get in without having signs of forced entry?
At the end, how does she get into the Gallagher home? Now, I know this one was probably easier to understand. Dan and Beth are upstairs in the bathroom for a few minutes. It would be easy to slip in. Periodically Dan is locking the doors around the house although he is being a little too casual about it as far as I am concerned. He knows Alex is out there somewhere. She kidnapped his daughter and boiled her bunny. She could do anything. So I am guessing she slips into the house before the doors are locked.
But during the day when the bunny boiler thing happened. Hmmm. Hard to say. Dan and Beth were gone all day. Unless they forgot to lock a door or something.