Animation production workflows often involve digital colorization of line art, where small unpainted regions (“gaps”) frequently occur and remain an underexplored challenge. We conducted a formative study in Japanese animation (anime) pipelines and found that while the paint bucket tool is widely used for base coloring, tiny enclosed areas are frequently overlooked, resulting in time-consuming manual detection and filling. We introduce GapFill, a tool grounded in professional practices that reduces the effort of gap detection, zooming, and color selection. Our deep-learning method suggests appropriate fill colors by referencing surrounding regions, leveraging the flat-color nature of anime-style images. In a user study with 13 professional colorists, our system improved performance and usability in gap-filling tasks over conventional methods. The study also suggested that prediction accuracy alone is not the primary factor for usability, that appropriate colors can be contextually ambiguous, and that GapFill can complement existing tools depending on users’ trust in new AI-powered assistance.