Via io9.com:

Jyn and Cassian facing off with Krennic. Bodhi working communications. Chirrut and Baze fighting on the beach. The space battle. The Imperials. And finally, Darth Vader and the ending. Trying to put the many, many pieces that are part of Rogue One’s third act together wasn’t quite as hard as stealing the Death Star plans, but it sure wasn’t easy

“It was a very complicated third act,” Rogue One editor John Gilroy told io9. “There’s a lot of things happening at the same time. Our characters are at different places in the movie and we’re cutting from one to the other to the other. And you had to keep things clear, but you had to keep things moving.”

Gilroy is one of three editors credited on Rogue One and was brought in well after principal production was completed. He explained that at some point the filmmakers had decided on a new direction for the movie (he wouldn’t discuss it beyond that, unfortunately) and he was brought in to execute that new vision.
“This movie was supposed to be different than other Star Wars movies,” he said. “They were trying to push the envelope of what a Star Wars movie could be. And when you do that, you try to walk that line. You want to make it different but you also want to very much make it part of the whole Star Wars saga. So trying to find that balance was the biggest challenge.”

Some of the changes were character additions at the beginning of the film (detailed in this article) which reverberated through the rest of the film, truly coming to a head in the third act.

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