Directors J.J. Abrams and Ryan Coogler made production notes for Ava DuVernay's A Wrinkle in Time that ended up affecting the final cut. A lot of times, filmmakers edit films across the hall from each other in editing bays. If it's at a major movie studio like Walt Disney Studios, then notable directors and editors could be cutting blockbuster movies literally next door, which is why, occasionally, directors tend to provide small but useful production notes or suggestions to their fellow filmmakers to better their final product that hits theaters.
For instance, Abrams had said on the commentary track for Star Wars: The Force Awakens that it was DuVernay's suggestion to give Rey (Daisy Ridley) an internal moment during the climactic lightsaber duel between her and Kylo Ren (Adam Driver) towards the end of the film. Then, Coogler had mentioned in Black Panther's commentary that Donald and Stephen Glover had offered suggestions to pump up some the film's comedy. So, it was only natural that DuVernay would receive a production note as well during the filming of A Wrinkle in Time, but this time, she received two suggestions: one from Abrams and one from Coogler.
Reese Witherspoon's introduction as Mrs. Whatsit is quite grounded in A Wrinkle in Time, but the filmmakers originally planned on making her entrance much more magical. J.J. Abrams suggested to Ava DuVernay that they hold off on front-loading the film with so much magic until after the characters tesser for the first time, that way the magic is more, well... magical for moviegoers. The production team went through multiple iterations trying to get Mrs. Whatsit's entrance down perfectly.
Later on in the film, there's an emotional moment when Meg Murray (Storm Reid) finally finds her father, Dr. Murray (Chris Pine). Ava DuVernay says in the film's commentary that she showed Ryan Coogler an early cut of A Wrinkle in Time while she was editing the film at Disney, just down the hall from Coogler and his team editing Marvel's Black Panther. That's when Coogler told DuVernay that he wanted to see more of the father so that, when he reunites with his daughter, it's an emotional feeling for the audiences as much as it is for the characters. That's why the editing team added a few flashback sequences earlier on in the film so that audiences would be familiar with the father and his relationship with his family.
While the end product wasn't as well-received as the filmmakers would've hoped, A Wrinkle in Time still had some redeemable parts to it, according to critics. One of those aspects was the core story centered on the Murray family, not to mention some of the performances - and the long-awaited meeting between Meg and her father was one of the moments that was more emotional and well-rounded compared to the rest of the film.