Warning: Contains spoilers for Encanto.
Disney is no stranger to making their animated films, targeted primarily at children, secretly imbued with bigger and more adult storylines, and magical house, Casita, appears to Abuela Alma after tragedy strikes and her husband is killed in conflict, and Abuela flees to safety with her triplets. The family grows larger over the years and each member gets a gift, except for Mirabel. This leads Abuela to be overly harsh on her, but, she is actually harsher on Isabela.
The crux of Encanto is that, due to her own trauma, Abuela Alma places too much pressure on her family. The film's ending shows her and Mirabel reconciling, and she explains why she clings so hard to her family and holds them to certain expectations. Before this, though, Abuela does treat them very sternly, almost micromanaging the Madrigal family's gifts, being especially hard on Isabela.
The reason for this could be the fact that Isabela is the family member who most strikingly resembles Abuela Alma when she was younger. They have nearly the same face, and a small picture of a young Isabela with her door shows her wearing two plaits in her hair, exactly like Abuela did when she was young. This physical resemblance results in Isabela reminding Abuela of her trauma, thus being especially hard on her, rather than Mirabel as the film leads audiences to believe.
Isabela's narrative is a big part of the film, concerning her potential engagement to Mariano. This places a lot of stress on her, most of which stems from Abuela. Isabela confesses to Mirabel that she doesn't want to marry Mariano, which deconstructs a huge Disney tradition, and shows just how far she's pushed to be perfect in the eyes of her Abuela, that she would go through with a marriage she doesn't want. Whilst Mirabel is treated unfairly, she is not pushed to such an extreme as her sister. Another small example of the perfection pushed onto Isabela is a small scene where she conjures some flowers in her hair. All of them are pink, except for one white one. As soon as Abuela sees this, she nonchalantly plucks the white one from the bunch so the rest of them are cohesive and polished. This small instance of micromanaging over Isabela's appearance, and then her relationships, shows the extent to which Abuela is the hardest on Isabela.
Abuela's actions stem from her own incomparable and heart-wrenching trauma. Encanto doesn't villainize her, but reflects real human experience regarding breaking generational cycles of trauma. The resolution of the film - which sees her explain this and apologize, learning to be better, gives a different kind of ending to Encanto.