#9 The Mother’s Disease
The audience never actually got to know about the illness that killed the mother. Ted is surely telling stories about how he met their kid’s mother and might be the kids knew it as well, but the audience was never told about that.
#8 Barney's Baby Mama
Barney is taking care of his baby, wouldn't that mean that the baby's mother would be in the picture in some way? Unless Barney fought for full custody of the baby, we should have met "No. 31" as Barney so lovingly put her or at the very least learned her name.
#7 Gary Blauman
In the episode, “The Chain of Screamingâ€, Barney tells a story about a Gary Blauman who apparently yelled at his boss and then quit his job. And after that, he fell into ruin and later killed himself, but see him again many times in the series. Was Barney lying or was it just a writer’s mistake?
#6 Marshall's Time In Rome + Other Finale Story Lines
The finale was so rushed that we never actually got to know the whole story about the things that happen after Ted meets the mother.
#5 The Mother As Ted's Soulmate
The Mother As Ted's Soulmate Since we spent most watching Robin and Ted onscreen and moving over them to finally meet the mother, Tracy, we as the audience have our confusions about whether Tracy is Ted’s actual soulmate or not. Also, it’s difficult to imagine Ted spending rest of his life with Robin even when it’s six years since Tracy died especially after him telling his kids this story about meeting their mother and them realizing he's been in love with Robin this whole time.
#4 Marshall's Fighting Knowledge
While in the earlier episode, Marshall has told about how he knows nothing about fights, but later, he tells that he has fought a lot with his brothers. Some people might say that he doesn't consider fighting with his brothers as real fighting, but he uses the fighting with his brothers as his proof in "The Fight." That's a plot hole and continuity error if I've ever heard one.
#3 Lily's Relationship With Her Father
Why does Lily say that her father would never pay for another wedding in a Season 2 episode when she's been estranged from him for so long according to the "Slapsgiving 2" episode? Plus, how would Mickey have paid for Lily's wedding if he was a failed board game designer?
#2 Lily's Mother
Though she lives in New York, she never comes frequently to see Lily. We see Lily's mother maybe only twice throughout the series and yet Mickey pops up many times, especially in the later seasons, and even goes to Rome with Lily and Marshall.
#1 What Happened With The Damn Pineapple?
This is the biggest plot hole of the entire series, the final season was so rushed that it left a lot many plots loose. The How I Met Your Mother complete series DVD collection, “The Complete Story,†has a deleted scene explaining the pineapple, but WHY ON EARTH was this not included in the actual show? And since it is not included in the main series, it is considered a plot hole.
