There's no definitive canon answer in the film canon that I know of (including on any of the extra features on DH2 Blue-Ray, interviews, or the script).
However, in DH2 film, Death Eaters are able to Apparate around the castle during the battle (and Voldemort, when fighting Harry as well); meaning that the Anti-Apparation Jinx isn't in effect anymore.
Possible explanations are that:
Voldemort had managed to break the Anti-Disapparation spells when he broke the wards
Or they were sabotaged by Snape earlier on his orders, acting as Headmaster. As we can see from Half-Blood Prince movie script, Harry and Dumbledore Apparated at the Astronomy Tower, and Dumbledore told Harry he can open/close "windows" for apparation, as Headmaster:
DUMBLEDORE: Take my arm.
HARRY: Sir, I thought one couldn'ta apparate within Hogwarts.
DUMBLEDORE: Being me has its privileges.
EXT. ASTRONOMY TOWER - NIGHT (MOMENTS LATER)
Harry and Dumbledore materialize on the rooftop ...
Harry ... sees Dumbledore MUTTERING WEARILY as he GESTICULATES with his blackened hand.
HARRY: Sir, are you... praying?
DUMBLEDORE: (smiling faintly) No, Harry. I do not pray. I was merely closing a window -- the one that had allowed us to Apparate.