Colin O'Donoghue (Captain Hook) broke his foot in the previous episode. When he's standing at the bottom of the beanstalk in this episode, you can see his left foot is larger, due to the cast.
In this new reality the black fairy is Henrys adoptive mother. She is also biologically his great-grandmother through his father. In Henrys reality Regina who is his adoptive mother is his step-great grandmother being the step-mother of his grandmother Snow White.
When we first cut to Emma in the hospital, she is painting a swan (her namesake).
Emma doing chin-ups in her cell mimics Sarah Connor in Terminator 2 (1991).
Where Hook and David are talking near the beanstalk, the camera pans out and you can see a black cast on Colin O'Donoghue (Hook)'s foot from when he broke it in the previous episode shooting.