For Chinese literature, this tends to happen to the main characters in modern Asian adaptations of Jin Yong's work. One rather noticeable example can be found in a 2008 adaptation of Legend of the Condor Heroes, where the protagonist Guo Jing is played by teen idol and heart throb Hu Ge. Guo Jing is normally described as being a rather stout, muscular man who is not exactly known for being incredibly handsome or refined. Hu Ge, on the other hand, is a Real Life equivalent of a Bishōnen. Needless to say, it can be rather unnerving for certain fans to see other characters mention how "manly" and "plain" Guo Jing is, when he◊ looks◊ prettier◊ than some of the female cast.
Bridge of Birds has an in-universe example: Lotus Cloud is described as not being conventionally beautiful, having "thick legs" and a "flat face" and her only exceptional feature being her bewitching grin, but the ancient myth about her true goddess identity describes her as "the most beautiful girl in the world". When this discrepancy is pointed out to Master Li, he dismisses it as a "mere literary convention" and says that physical beauty has always been a highly overvalued trait.
The Doctor WhoEighth Doctor Adventures novels tend to describe the Eighth Doctor, played on the show by Paul McGann, as tall, skinny bishonen. McGann is 5'8" and 160 lbs, with a solid build. To put this into context, he only has a couple of inches on the Second and Seventh Doctors (Patrick Troughton and Sylvester McCoy), who are canonically seen as "funny little men". (Publicity photos for the TV Movie, however, had McGann standing on a box so that he appeared more substantially taller than McCoy; the resulting staged imagery may have been the origin point for this trope in the books.)
The books tend to describe the Fourth Doctor as thin as well. Tom Baker was quite thin when he was first cast for real life reasons, but took on a more solid build soon after.
The First Doctor is commonly described as imposingly tall, when he's 174cm tall, the same height as Paul McGann and about an inch taller than the Second Doctor, considered to be short and weird-looking. The fact that the Second Doctor wore baggy versions of the First Doctor's clothes in the show and has a symbolic scene of him losing his ring from his now small fingers may make this a case of Informed Attractiveness as well.
Jon Pertwee was sensitive about his large nose and used to request all illustrators making images of him draw it smaller as part of the deal for using his likeness. This affected the Target book covers, contemporary comics, and other such ephemera like the promotional deal Doctor Who made with Sugar Smacks cereal.
The 1979 Annual described the Fourth Doctor as 'handsome' in one story. He's far from unattractive, but 'handsome' is a major stretch.
The book version of "Shada" has Chris describe Romana as 'the most beautiful woman he had ever seen' as part of his initial description of her, which is a description hard for anyone to live up to, even the gorgeous Lalla Ward. However, he notes that he doesn't find her sexually attractive, but awesome. The Animated Adaptation of "Shada" makes Chronotis rather more handsome and makes Clare into a punk with pink hair, leather and studs. And the Big Finish version runs up against it accidentally - replacing the very weird-looking Fourth Doctor with the conventionally handsome Eighth Doctor.
In-universe example in Mortal Engines: When Pennyroyal writes a book about his travels with the protagonist, Hester finds an illustration of her counterpart in the story. Hester has a large disfiguring facial scar that's destroyed her nose and cost her an eye, the scar tissue has further twisted her face. Her counterpart is a beautiful air pirate with an eye patch and light cheek scar. Despite this, the (real) film adaptation appears to have gone down a similar route, based on its trailer - the lower half of Hester's face is covered by a cloth, but she still has both eyes and no sign of scarring at all on the visible part of her face. This appears to be the most controversial part of the otherwise rather well-received announcement.
Elphaba from Wicked is based off the MGM version of the Wicked Witch of the West. While she's still lanky and boney, and has a large nose, she's considerably less warty and unattractive.