The Aurabesh lettering and the rest of the van's graphics on the side door are completely devoid of color while they're at the Texas coffee shop; the rest of the time the graphics and lettering have color.
When the tire of the van blew up it was the front right tire. In the next scene with the van veering to the right and crashing, you can see that the front right tire didn't blow up.
When The Chief is giving Linus the illegal drugs, there is writing on the back right tire. In the next scene when Windows is yelling that he is a pedophile, there isn't any writing on it anymore.
When Windows is declaring Harrison Ford as the greatest actor of all time, the group drives past a sign for the movie Six Days Seven Nights (1998) which reads, "Escape June 12". However, the film was released on June 14, 1998 while the events of this film begin on October 31, 1998.
When everyone is being chased through Skywalker Ranch and jump down a garbage chute, Hutch dives in head first but when he exits he comes out feet first. This was regarded as an error but it is likely the director purposefully did this to spoof Star Wars: Episode IV - A New Hope (1977), in which Han jumps in head first and comes out feet first.
When Eric approaches his old friends at the party, Windows says "god, it's been parsecs". A Parsec is a measure of distance, Not time. This is deliberate, as it was also an error made by Han Solo in Star Wars Episode IV: A New Hope.
In the opening sequence when we see the words come across the screen it states "the year is 1998". On the bottom it says "sent from my iPhone". The film is told as a story, so the crawl would have been written later.
On each side of Hutch's Star Wars van there are clearly visible markings written in Aurabesh or New Aurabesh which is the common writing system for the Basic (our English equivalent) language in the Star Wars universe. Basic is read the same fashion as English (top to bottom, left to right). Translating these writings we see the word "SYOBNAF" on both sides of the van. "FANBOYS" spelled backwards.
The shot of the projector has been reversed: projectors feed downward.
When they are arguing with the Trekkies in Riverside, Oregon, the guy dressed as Spock has the ears on upside down.
When they show the projector the movie is threaded upside down. The thick blue line is the soundtrack which goes at the top not the bottom of the piece of film.
As the fanboys are escaping with Hutch's van from their encounter with Star Trek fans in Riverside, Hutch is seen climbing into the driver's seat. However, in the next shot, a flash of sunlight reveals the driver to be another man, definitely not Hutch or one of the fanboys.
Linus, Hutch, Windows and Zoe watch the Stargate SG-1 (1997) episodes Small Victories (2000) and Double Jeopardy (2001) in 1999. However, these episodes were first broadcast on June 30, 2000 and February 16, 2001 respectively.
Quite a lot of the merchandise displayed in the movie was not released in 1998. Most noticeably the Master Replica Force FX Sabers (2005) throughout the movie (held by the Darth Vader statue, used by fans in the theatre), and the 12" Taun Taun in the 2002 "Saga" collection packaging in Eric's bedroom.
None of the fans would have the Force FX Lightsabers, which didn't come out until the release of Star Wars: Episode II - Attack of the Clones (2002).
There's an advertisement in the comic shop for the film Mirrormask (2005), which didn't come out until 2005.
In the first scene in the comic book store, Hutch is seen with a Mountain Dew can that has the release-era (2008/9) logo, not the period correct logo.
When the group arrives at the "Smith Ranch Road" exit, they are taking the exit from Northbound 101 and proceed to turn left onto Lucas Valley Road (Westbound) towards "The Lucas Ranch", however in the next few shots, they are seen passing a rock located on their left. That rock is a prominent marker on Lucas Valley Road and would have to be on their right if they were headed westbound towards the ranch.
When they plan to leave, they say that taking "Highway 80" is the fastest route. There is no highway 80 heading west from Ohio to Texas. There only Interstate 80, which is not even close to going through Texas. So, when they arrive in Iowa and argue about taking the longer route they actually went the way they discussed when they agreed to go, by driving Interstate 80.
When Hutch 'detours' into Iowa, he passes under a highway sign for Interstate 40 (visible through the windshield). I-40 runs roughly 900 miles further south than the Ohio-Iowa corridor.
While in the future birthplace of James T. Kirk, the Trekker says that "Captain Picard is not gay, he's British." The actor who plays Captain Picard is British, but the character is French.