(at around 6 mins) When we first see the angry cop, he looks at a wanted poster. This is an image of Junji Ito, the creator of the manga Uzumaki (2000).
The movie was filmed before the manga completed its run, revealing a different ending and new storylines not in the manga.
Spiral numbers 6 and 9 can be seen on several occasions, including on the license plate of the reporter's car, as room number in the hospital, and as a date in a video recording at the end of the movie.
Some areas of the screen are digitally twisted into a spiral pattern: in the first sunset sky; on the top right in a bird's eye view of Kirie and Shuichi returning home from school; on the ground when Kirie's walking over to Shuichi's house with a gift.
(at around 42 mins) A ghostly imprint of Kirie's face appears in the middle of the screen when she walks into Shuichi's house. This is the same face as when she's watching his father's grisly video recording.