"Everything is intentional," says Charlie in this interview with The Verge's Tasha Robinson. "Especially in a movie that's animated. There are absolutely no accidents, because it's happening one frame at a time."

What gave you the most technical problems as you were designing the film together?

Duke Johnson: Well, a lot of different technical problems came out of a lack of money. But mostly, specifically, it came out of a desire to want to have the most articulate-able puppets and the broadest range of emotions for the character performances. Typically, with low-budget stop-motion, you can get away with a cartoony style. But we wanted to have this authentic human experience, that's what we were going for, so it lent itself more toward a realistic aesthetic. So the level of nuance and detail goes up, so we had to figure out how to make these puppets relatable in a way that made that possible. Typically, stop-motion puppets can cost upward of $80,000. We had $100,000 initially to design all the puppets in the movie. So we had to find creative ways to do that.

[...]

The production studio Laika prefers to have individual animators tackle entire scenes, to enhance the continuity and give the scenes individual character. When I interviewed the directors of The Boxtrolls, I found out they had one ballroom scene done by a single animator who worked solely on that for 18 months. Do you prefer that method? Does it matter to you?

Johnson: That's ideal. It's an ideal scenario to keep one animator on a scene, because animators are like designers and actors. They have their own skill sets, and their own styles. But we didn't really have the luxury to do that on this film. We had animators coming and going, because we couldn't really afford to pay Laika rates. So we could only afford to keep animators a short period of time before they had to move on and take higher-paying jobs. And we didn't have the luxury of time — some of the scenes in this movie are extraordinarily long. Like, the hotel-room scene took the entire two-year duration of production to shoot, and we did it on multiple stages. So we had to put a lot of time into establishing these characters, and how they move, and what their specific character traits are, so all the animators could create a sense of solidarity. (Source)