(at around 47 mins) When Holden first tells Banky he loves Alyssa, Holden takes a drag on his cigarette and never exhales. He even talks a minute later with no smoke coming out of his mouth.
(at around 1h 16 mins) During the hockey fight #12's helmet is off, then on, then off again.
(at around 56 mins) When Holden and Alyssa leave their car after it had been raining for a while and argue outside, the road under the car is completely dry as though it had begun raining after the car was parked.
(at around 46 mins) When Banky is drawing an intersection illustrating why a man hating lesbian would be the one to get the $100 bill, he initially draws two complete intersecting streets. The camera then changes to a shot of him and Holden where he clearly pencils in two lines of the horizontal street which he has already sketched.
(at around 37 mins) When Alyssa and Holden are discussing the definition of a virgin, one of Alyssa's necklaces appears and disappears behind her shirt.
(at around 1h 10 mins) When Holden and Hooper are in the record store, several albums are shown to be misplaced in the wrong sections (The Beatles in the New Age section, Green Day and Faith No More in the Reggae section, Pearl Jam and Alice in Chains in the Ska section, Sepultura in the Big Band section, Fugazi in the Jazz section, etc.)
(at around 55 mins) While Holden and Alyssa argue in the rain, they are standing in front of an alley where it is clearly not raining.
(at around 13 mins) While Holden and Amy are throwing darts at the bar in front of the restrooms, only men are using the women's room and only women are using the men's room.
(at around 1h 12 mins) Hooper-X is asked to sign the little boy's comic book at the record store, and as the boy walks away, the comic book is seen to be an Avengers comic (the advertisement on the back indicates that it is from the early-to-mid '80s).
(at around 56 mins) When Holden is walking back to his car shortly after Alyssa leaves him in the rain, the camera crew is reflected in the window slightly to the left of Holden.
(at around 11 mins) Holden's radio mike is visible under his shirt in the CD store when he's talking to Hooper.
(at around 50 mins) The scene with Holden and Alyssa is shot on a two-way street from inside the car, but a one way street when they get out of the car. Also, they are going the wrong way on that street (just before they get back into the car a street sign is visible over the roof of the car).
(at around 26 mins) When Banky and Alyssa are sharing "oral sex injuries" tales, Banky comments that he can't move his head very far on the right. But right before, when Alyssa is kissing Kim, and he realizes he's in a gay bar, he tilts his head to the right (which is a constant Jason Lee move).
(at around 1h 30 mins) When Holden is looking at Alyssa's yearbook in the park, her photo is next to some guy with the last name beginning with P, Alyssa's last name is Jones.
(at around 1h 17 mins) Before confessing the Finger Cuffs story in its entirety to Holden, Alyssa says that she and Rick used to hang out with her sisters. In the film Clerks (1994) her sister Heather has heard of him but doesn't know who he is by sight and acts she's never met him when he tells her his name.
Towards the end of the movie when Holden is talking to Alyssa, he says (of the Chasing Amy comic book), "it was a small print run, only about 500 issues." Holden and Alyssa are in the biz, and would have said copies. Issues are what comes out each month, copies are the print run for each issue.
(at around 58 mins) Banky says to Holden "I wanted to watch some T.V. Hard to do when your best friend's wrapped around his naked rug muncher on your couch." Neither Holden or Alyssa Jones were naked when they were wrapped in the rug. They both has clothes on.