Dexter in the Dark, the third Dexter novel, shifted the series from crime thriller to supernatural horror, revealing the reason Dexter kills is because the spawn of an Eldritch Abomination (which comes complete with its own cult) has taken him as its host. The later novels make only minor references to these events, if that.
While plot and symbolism are often integrated in The Divine Comedy, Purgatorio Canto 29 and 32 both stop Dante's travels in their place to have him witness a series of strange events with no bearing on the rest of his journey. The only significance of this events are as symbolic tellings of the history of the Church, but this is the only place in which symbolism occurs with no parallel plot advancement.
The third story in Flashman and the Tiger, where the title character runs into Sherlock Holmes, Watson and their antagonist Sebastian "Tiger" Moran. For a series otherwise confined to real historical events, it's a jarring entry that's considered divisive among Flashman fans.
The book I Live In Your Basement!, due to copious amounts of mindfuckery and gorn. Even the ending where the whole thing turns out to be a basement monster's dream doesn't smooth out how weird this story is.
The Mog book "Mog and the Granny" is kind of a normal Mog book: the title cat's owners visit America while she stays with Debbie and Nicky's granny. However, it has a subplot where Mog has Psychic Powers: she always knows where Debbie is. This ability has never been stated before or since.
"Legend of the Cheese Maidens", which the authors admit was originally intended to be a non-canon erotic story that went off the rails, starts in the bedroom of two of the heroes (a married couple) talking about their sexual turn-ons, but then devolves into a peculiar story involving cheerleaders, space aliens, and urban legends.
"Lady Luck" is about a pair of thieves who take their pet goldfish, in a bowl, with them on a bank robbery because they believe it will bring them good luck.
Shusaku Endo's short story anthology Stained Glass Elegies consists of deadly serious examinations of Catholic faith in everyday life...and an over-the-top, sidesplitting parody of Fantastic Voyage. It was apparently the only comedy story Endo ever wrote, which makes the transition from thoughtful treatises to enema jokes all the more jarring.