Blackbeard's crew is actually shown attacking early on.
Robin's naturally muted reactions causes some early jokes to fall flat when there isn't anyone to react to them.
What starts the gun fight is when a man in the crowd shoots at the Thousand Sunny and this angers Franky. A shot is fired that hits Luffy, but there is no bounce back of a bullet. The scene shows Luffy thinking of a sick Nami and he bows of his own accord. In the anime it was Vivi who was shot and convinced Luffy to consider what would happen to Nami.
From when the crew first come across Drum Island. Luffy noticed the cold right away. Before, he didn't notice until someone asked him if he felt cold. On a similar note. Zoro is actually appropriately dressed for the climate the whole episode.
Zoro uses three of his meitous (named blades) in the fight against Wapol's men, but in the manga, when Franky had just joined. Zoro only had two swords. He didn't claim a third until after Brook had joined.
When Nami agrees to let Luffy take her up the mountain in the anime. It was one of the few times Nami ever called Luffy "Captain" in English. Here, she has a new line.
In the anime Vivi stayed behind in the city because she knew she would just slow down Luffy and Sanji. Here, Robin wishes to go with them, but Sanji tells her that it would be better with fewer people. It's never explained why.
The Isshin 20 turn on Wapol from the start and Dalton is never seriously injured.
The avalanche is no longer caused by the Lapahn, but by Wapol trying to make a flashy entrance into town.
Nami asks Doctor Kureha about the time it takes for the Log Pose to lock in Drum Island, but she seems to be in some sort of hurry. It's never explained why she's in such a rush. In the anime/manga story they were on their way to Alabasta.
A noticeable difference to this movie and some of the previous is the absence of Nami's perpetually bouncing breasts. Seeing how there is an abundance of clothing for Drum Island and she is sick through the first half of the film. Her fan service status is greatly diminished.