(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 Spiral (2000).
The movie was filmed before the manga had completed its run, and reveals a different ending and origins storyline than that featured in the manga.
6 and 9, being nearly spiral numbers, can be seen on several occasions: e.g. on the license plate of the reporter's car, as room number in the hospital, as a date in a video recording at the end of the movie etc.
Some areas of the screen are digitally twisted into a spiral pattern at least five times in the movie (not necessarily in this order): the first time you see the sunset sky, on the top right a bird's eye view of Kirie and Shuichi returning home from school, on the ground to their right to Kirie's left in the bushes when she's walking over to Shuichi's house with a gift a ceiling panel to the right of the stairs in Kirie's house as she walks down at night the end of the hospital hall, dead center.
(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 looking for his father, and is the same face as when she's watching his father's grisly video recording.