1) The Knights of the Old Republic series before TOR. TOR erased all of my choices from the first two games and (I feel) showed considerable disrespect to the characters of the first two games- particularly galling when the second game-which lacked a data import feature-still let players determine how the previous game played out through dialogue.
2) The Baldur's Gate Saga... Wizard of the Coast pretty much spit in the eye of every fan of the game with the godawful novelizations, but then years later when they decided to bring the setting-Forgotten Realms-into 5th edition, they decided to revisit that awful dross and reafirm its place in canon for all time. Not only is Abdel confirmed, once again, to be the canon Bhaalspawn, but his deeds (the player's) are deliberately downplayed, before he gets assassinated by a gag character whose defining trait from the games was his cowardice. Shortly afterward, the evil god Bhaal is reborn from the essence of his slain children. So the player character's soul is destroyed forever and everything you worked for over the entire Baldur's Gate trilogy is wiped out.
But hey, Minsc got a statue, so I guess fans of the series are supposed to be grateful or something?
3) Geneforge III....(spoilers)... Playing Rebel-aligned in that game in particular just seems like such a betrayal. They use creations as cannon fodder despite their stated position of creations being equal to humans, they use dangerous, disfiguring, mentally damaging mutagens as an irresponsible shortcut to magical powers and which they have engineered addictive qualities for recruitment purposes. And if you do decide to drink the cool aid and join their faction in order to improve the quality of life for creations, you'll have to become complicit in the murder of prisoners of war, (you actually have to murder a nearby high-ranking member of the Shaper Order-one with rebel-sympathies, no less-so the rebels can execute some shaper hostages without fearing reprisal from said Shaper.) Post game you go on to aid in the massacre of many, many shapers and anyone who harbors or sympathises with them. Unfortunately, that's canon. (end spoilers)
Honorable mention goes to Skyrim and Fallout New Vegas, for using gender-neutral pronouns throughout the entire game to refer to previous protagonists (Morrowind, Fallout II), only to throw it away in a single dialogue...why even bother going through all that trouble like that if you are going to drop the pretext of leaving it up to the player's imagination at the last minute?