After hearing about the twist and looking closely at the picture of Esther realizing "Holy shit she does have age marks!"
There's a lot that will make you say "holy shit!" on a second viewing. Why does she prefer to wear Victorian dresses over blue jeans? To hide her more "adult" figure. Her avoidance of doctor and dentist appointments. "I've had a lot of time to practice, I guess." "She's very mature for her age." There are even subtler moments like when Kate is yelling for Esther to hurry up on her first day of school...perhaps she was taking so long because she was putting on all her makeup.
Here's a subtle one: Danny notices Esther cuts her food into little pieces before eating anything. It could just be her style of eating, but it makes a lot more sense when you find out that she's wearing false teeth and eating with them in would probably be very difficult without cutting things very small.
Esther's pretending to be Russian makes even more sense when you take in her actual age as Leena. Leena was born in what was still the Soviet Union, meaning she could very likely have gone to a Russian school and been fluent in the language. Estonia is a very tiny country, especially in population, and by saying that she's from Russia that gives a huge amount of possible ground to cover in finding out where Leena's actually from. Meanwhile she wouldn't have to worry about being questioned in Russian because that was a state language.
Orphan First Kill: Esther's therapist sessions. According the second movie, true little Esther was visiting the same therapist. For what reason does a child this young need a therapist so soon? Given Gunnar's weird behavior (possible psychopath, who was clearly not feeling too guilty about killing his own sister) it's not hard to guess why would a three-year-old girl need special help. Psychopaths don't just abuse their siblings, they basically torture them (just like little animals). This gives an even worse point of view on Tricia, who would probably even hide her son's abuse towards real Esther.
The scene where Esther goes to the hospital for her broken arm. In real life, the doctors would have easily discovered the bones belonged to an adult dwarf and not a little girl.
How did Esther arrive at the American orphanage without having been brought by someone? Even if she forged her paperwork, she couldn't just show up at the door with it by herself. And how did she manage to avoid medical exams the whole time she was there?
Well now we have Orphan First Kill to explain that how she was brought to an American orphanage. She impersonated a missing child of a rich American family, and after killing the family and burning down their house, she was "found" by the police and firefighters, and taken to an orphanage
In the prequel, what was Tricia's long-term plan for keeping Leena around as a cover for Esther's murder? Eventually, people, first of all Allen, would notice "Esther" wasn't aging and it'd be almost impossible to stage Leena's death without inviting any suspicion—any benefit of the doubt they've run on from the "disappearance" would likely evaporate instantly the "second" time Esther was subject to an incident.