Continuity mistake: In Ted's flashback where Barney's mysterious saboteur is talking to Lily, the girl has straight blonde hair. In episode 14, "The Bracket" where his saboteur was first introduced and she originally spoke to Lily, she had curly blonde hair in the same sequence.
How I Met Everyone Else - S3-E5
Factual error: When Ted is talking about what Marshall told him after he met Lilly, the two boys are playing with Playstation 2 controllers. The scene takes place in 1996, and Playstation 2 didn't come out until 2000.
How I Met Everyone Else - S3-E5
Other mistake: In the scene where Barney is describing The Vicky Mendoza Diagonal of The Hot-Crazy Scale, his words describe her getting hotter, (i.e. lost ten pounds) not less crazy. On the diagram shown, she goes down in craziness, not up in hotness.
The Chain Of Screaming - S3-E15
Audio problem: At the very beginning, after Ted says, "A new car", Lily's lips move, but she doesn't say anything. Obviously her dialogue was cut in post-production. (00:00:10)
Continuity mistake: In this episode we get to see when Barney lost his virginity to Rhonda, The Man Maker. They had sex in her bed. But in season 2 (12th episode, First Time In New York), Barney says that his comforter smelled like menthol for a week.
Slapsgiving - S3-E9
Continuity mistake: Marshall turns on the computer, and a readout pops up clearly displaying 2h 45m left on the countdown. He then says "look at that - that means we're in the final hour left of the countdown".
Continuity mistake: When Lily is selling her favourite dress and is saying how she got a two syllable damn, the flashback shows her with the hairstyle she got after Coming Back from San Francisco, even though she said it happened in 2004. She should have had her shorter, lighter coloured hair. (00:15:10)
Slapsgiving - S3-E9
Revealing mistake: When Marshall slaps Barney in Slapsgiving you can see that his hand doesn't actually touch Barney's face and there is no audio to match the slap.
Other mistake: In the flashback where Gael is playing a guitar and singing a song, the chords on the guitar change, but his fingers do not move at all. He is playing the same chord the whole time.
Sandcastles in the Sand - S3-E16
Continuity mistake: When Lily goes to the bar with her friend Michelle, Barney says "I want her around all the time." It then cuts from Barney to Lily's slightly shocked looking face, obviously from a previous cut/scene change, sitting at the table with them - she should still be walking to the bar with Michelle.
Suggested correction: Those were different days. Robin agrees to watch Simon's practice before we see Michelle the first time, then the scene cuts to Robin watching the band practice, then the news feed and then the next scene with Michelle. All the character's clothes changed indicating a different time.
Dowisetrepla - S3-E7
Character mistake: In the scene where Robin and Lily are talking in the kitchen, Robin makes a reference to Mount Waddington being the tallest mountain in Canada. The tallest mountain in Canada is actually Mount Logan.
How I Met Everyone Else - S3-E5
Continuity mistake: During the flashback in which Barney recounts the story of how he and Ted met (which was previously shown in the pilot episode of the series), there is a green circular plaque (that reads "Winner of the Queen Cup") on the wall in the background which wasn't present in the pilot episode. Also, Barney's left arm is in different positions than it was in the pilot.
Continuity mistake: When Robin buys Lily's "favorite dress", Lily holds it on her lap folded, when the camera changes angles it is unfolded.
Continuity mistake: Barney blocks Ted's path by standing in front of the door. Watch his position as he says, "Ted, don't do this" for the second time, he has his right arm over his head. When the camera changes angles he has it down.
The Chain Of Screaming - S3-E15
Continuity mistake: The ice cream Robin's eating in Ted's car keeps changing shapes between shots.
Continuity mistake: When Ted, Barney and their dates are in the tub, Barney is holding a bottle. He takes a sip (i.e. no cap) and hands it to Amy (Ted's date). Now it has a cap. She hands it to Ted who unscrews it and has a drink.
Continuity mistake: When Barney and Abby are lying in bed after the Local Art Cafe scene, Abby's arms/hands change positions between shots.
No Tomorrow - S3-E12
Continuity mistake: At the Saint Patrick's Day party when Barney says, "it's not cheating if her name has two adjacent vowels" his right hand is up near his left hand, pointing to his fingers. When the camera angle changes his hand is back at his stomach.
Continuity mistake: When Ted, Barney and the girls are heading to the South Bronx in the cab, keep watching Colleen's head, near when Barney says, "Somebody's been watching too many Seinfeld reruns", her head moves instantly between shots, from looking towards Ted to looking at Barney.