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After Penny doesn't get adopted while other kids are, Rufus tries to comfort her with "Faith is a Bluebird". She is convinced of her own homeliness nevertheless, making it all the more devastating that a child her age could have such heavy self-image issues.
Take a close look at the room Penny's staying in during her time in Devil's Bayou. There is a poster on the wall with stick figures, depicting her with a mom and dad. Don't cry, don't cry..
Could either be her actual mom and dad (if she remembers them), or an imagined drawing of the parents she wishes she had. The latter is a bit less heart-wrenching, but not much.
The song "The Journey" during the beginning credits. Something about watching the bottle be tossed in the ocean as the music wells up dramatically, just emphasizes how helpless Penny must feel.
Penny's breakdown after she prays for someone to find her.
Penny: Please let someone find my bottle, there's a message in it. Because running away isn't working. Amen. [Addressing her bear] Don't worry, Teddy, we'll be... alright... [collapses into tears]
Thankfully, Bernard and Bianca have just made it to her room and can reassure her.
Cody asks Marahute, "Where's the daddy eagle?" She just bows her head in sadness, to which he says:
Later on, McLeach outright tells Cody he was the one responsible for killing the father.
When the Rangers come to the house of Cody's mother to tell her he was eaten by crocodiles, the gestures of the mother tell it all.