The two big give aways for me, are that they supposedly declared that she had been "taken by someone" immediately when the only thing that had happened was that she was missing. Most people's first assumption would be that a child had wandered off looking for them / was lost, not a random kidnapping, especially as the other two children were still safe.
Second thing is that they kept insisting on a narrative where the window had been forced open for someone to get in, and then when informed that the sequence of events was impossible, suddenly changed the story to the door being left unlocked.
Straight away none of it adds up. Trying to figure out what DID happen is really mostly speculation, obviously, but you can be pretty sure that there's a lot more to what happened that night than they've ever said, just based on their inconsistencies and changing stories, and other very odd statements from various people.