When Lee decodes the inverted triangle in the library, the circled dates change between shots with the first version not fitting into the inverted triangle theory.
When Lee first visits her mother, she observes a cockroach emerge from underneath the closed basement door. Stacks of canned food are seen on the floor beside the refrigerator near the doorway. However, in the next shot when Lee approaches the door, the cans are no longer there.
The first time Harker is at her house it shows the front door top lock chain locked. Moments later there is a tense moment where she locks the same chain lock.
When Carter's wife invites Harker into their house for Ruby's birthday, she holds her left hand. But in the next shot, she is seen holding her right hand.
When Lee visits her mother and they are sitting on the bed speaking right around the 59 minute mark, The mother is wrapped in some type of sweater or shawl. However, when the camera is fixed on Lee, you can tell by looking at the mother's arm that she is wearing the sweater or shawl in a completely different manner as the shirt or blouse underneath the sweater or shawl is visible in a manner inconsistent with the way the mother is wearing it when the camera is fixed on her.
When Carter & Harker are in the barn (eventually finding the doll), the lighting in the window appears as daytime, despite it being the middle of the night. However, the lighting is actually coming from the floodlights mounted to the exterior wall of the barn.
Numerous scenes include vehicles with plates depicting lavender mountains with a Douglas Fir tree in the middle. This design was not released until 1988, though the film is set in 1970s Oregon.
In the opening scene, and once later in the movie, a Common Loon call can be heard multiple times. While commonly used in films for its spooky sound, it is revealingly out of place here as it is winter - loons fly south for winter. These calls in the film are known as loon 'wails' and are used to communicate between pairs - if there is snow, there are not loons in the area, as these are breeding season calls.
When Lee decodes the letter she receives in her house from Longlegs, the number of letters/ symbols on the letter do not match up to her decoded message. When checked using Vigenère cipher (on the Longlegs Vigenère cipher website), the encryption for "head" is missing in the original message.
When Lee is driving the car to Carter's house near the end, the gear shift is clearly in the Park position. It's only when she pulls up to the house that the gear shift is in Drive.
When Lee Harker is driving to the Carter's house, the car's gear shift is in Park.
Despite the movie being set in the 1990s, the theme for "The Price is Right" that can be heard on the TV is the version that has been used since 2007.
Earlier in the film Harker is told that the killer doesn't leave behind any trace at crime scenes yet later on in the film the killer is clearly doing things (parking at crime scenes, entering homes) that would easily leave trace evidence.
Warning: Contains spoilers -
Since Longlegs can influence others, then it stands to reason that he could influence others to ignore, or just not see, any evidence that might have been left behind.
1:31:22, as Lee arrived at the Carter's, you can see a Porsche 911, likely a 996 model (produced 1999-2005), parked in their driveway.
When agents Harker and Carter uncover the doll buried beneath the floorboards in the barn, the number of lightning strikes in a row that were shown is unheard of for western Oregon in the winter, and most certainly was added for dramatic effect. While storms are common in western Oregon in the winter, lightning and thunder are not.