Continuity mistake: In the beginning of the series, Haley's big family is brought up often, implying that she has 3 brothers and 3 sisters. When her mom visits her, Taylor and Quin to announce that she is dying, there is no mention of or visit from any other siblings and Lydia talks about those 3 as if they are her only children.
Continuity mistake: When Lucas is with Keith at the graveyard in 4-10 and Brooke is standing in front of "Peyton's" tombstone, it says she died on March 1, 2006. Keith notes that she died on the day of the shooting. However in this episode Lucas visits Keith's grave where his tombstone says he died in January 2016.
Visible crew/equipment: When Lucas meets Peyton by his tow truck there's a crewmember wearing a green shirt with arms and legs visible next to him.
The Birth and Death of the Day - S4-E20
Plot hole: In season 4, Haley finds out she is pregnant. It is presumably around February, since it is right after Nathan and Haley's vow renewals and after the school shooting. If she, let's say, was already a few weeks along, she would not have given birth in June at graduation, but in October of the following year, since it takes 40 weeks or 9 months for a baby to go to full term, not 5 months.
The Worst Day Since Yesterday - S3-E8
Other mistake: At the start of season 3 it is established by Whitey that the lockers are in alphbetical order, hence why Nathan, Haley and Lucas all have lockers next to each other, but in this episode when Haley and Rachel decorated the Scott brother's lockers, Brooke then goes to her locker and is sad when she opens it as Lucas decorated it earlier in the season. Brooke's locker however is only a few lockers away from Lucas', even though they are meant to be in alphabetical order.
Visible crew/equipment: The scene where Lucas meets Payton on the side of the road with the tow-truck. Once they are ready to get into the truck you can see equipment in the middle of the road, as Payton starts walking towards Lucas. (00:28:50)
Searching for a Former Clarity - S6-E18
Continuity mistake: In the legendary "a random dog eats Dan's heart" scene, the cooler and its lid keep changing position between shots when they fall on the floor.
4 Years, 6 Months, 2 Days - S5-E1
Continuity mistake: When Hailey finds Nathan asleep on the couch and cleans up his mess she originally has 2 beers and a bottle of tequila, but in the next shot she has beer, tequila and chips.
Everything in Its Right Place - S4-E11
Character mistake: Brooke and Rachel are in the clean teen meeting and they are asked if they want to join. After both saying yes, the clean teen president hands them their shirts but calls Rachel Brooke, and Brooke Rachel. You can see their hair colors and they didn't change spots when she went to get the shirts.
Prom Night at Hater High - S4-E15
Continuity mistake: In this episode a sex tape shows a fling between Brooke and Nathan, and it is supposed to be from the past, but Nathan's hair is much longer and so obviously older in the video that it looks like it could have been filmed the night before, not from when he and Peyton were together.
Continuity mistake: In the final scene of the episode Brooke joins Mouth at the side of the Rivercourt, but when the camera switches to further away it shows Brooke walking towards Mouth and joining him again.
In da Club - S5-E7
Visible crew/equipment: Mic drops into the top left corner when Haley and Payton talk to Mia before she goes onstage.
With Arms Outstretched - S1-E9
Continuity mistake: When Lucas is showing Keith his tattoo, in each shot the sleeve of his shirt keeps changing from rolled up to rolled down.
Character mistake: During the state game, Mouth starts to announce information about the game. You can see him in the background, however, his mouth is closed and he isn't speaking until it changes to the next clip. (00:28:00)