Sophie's little brother was another one of the super-soldier kidsHe is very calm through the whole movie, and very observant, easily spotting Hanna in her hiding place but doing nothing to indicate shock or to blow her cover. Later, he wordlessly helps her sneak out of the van without drawing attention from his parents.
Marissa is actually Hanna's dad.Our introduction to her goon squad takes place in a transexual stripclub with several choice bits about the owner's preferences for, ah, performers. Here's a hint: He likes them with 'parts' from both men and women.
Marissa actually did have a genetically-enhanced baby of her own like Hanna, whom she had to kill.This moment was her Moral Event Horizon, and she therefore sees Hanna as the daughter she could have had. The last two points in the previous theory about Marissa being Hanna's transsexual father support this theory also, while alternately, many of the points listed below can also support that theory too. At any rate, it's at least implied that Marissa was indeed a parent at one point, or sees herself as one.
Marissa and Erik at one point were lovers.What with how obsessed Marissa is about being the one to personally kill Erik, despite her department's increasing annoyance, and their sexually-charged phone conversation.
Hanna is the clone Hannalore from Questionable Content theorized she might have.There's a physical resemblance but Hanna must have been made after Hanners to account for the age differences. This also explains the similarity of their names, as it would be confusing to have two clones with nearly the same name, but Hanna was clearly named after Hannalore. Hanners' mom and dad are Hanna's parents and the woman Erik considers to be Hanna's mother is just a surrogate, hence Marissa's laugh at the question of Hanna's parentage: not only do they not know who the father is, they don't even really know who the mother is.
Hanna is one of the clones created by Franchise.She's practically an albino in this. Given that she's the sole survivor of a cancelled project, the Franchise presumably used different cloning methods after her.
The German clown guy is Hanna's real father.He tells Hanna she "looks like her father", even though he should know Erik is not Hanna's biological father. Of course it's possible he just knew Hanna's real dad, but him being the real dad would explain why he's so friendly towards Hanna, and why he's willing to face death so that Hanna could escape Marissa and her henchmen.
Hanna is actually the reincarnation of Susie Salmon.
Hanna is a Sentinel.Her instincts and senses are all higher than the average human's. The program Erik was involved in was designed to artificially create Sentinels, as with their heightened senses they would make ideal super soldiers. Hanna's freakouts in response to modern noise were very similar to the sensory overload Sentinels go through. Hanna also became attached to Sophie, probably seeing Sophie as her Guide.