In most everything related to her, the Raven Queen from Dungeons & Dragons Fourth Edition is portrayed as a Kelemvor Expy who's True Neutral and represents death as a natural part of life and its inevitable end. Except for one sidebar in Divine Power, where she's suddenly a cacklingly evil madwoman who killed Nerull to take his place and was only forced into her current role by the other gods... who she wishes to overthrow so she can become a true Nerull Expy, seemingly for absolutely no other reason except that a goddess of deathmustbe evil.
It might have happened because she was such a popular choice for a deity for new players to 4.0, the Wot C wanted to dial back on her being too attractive to all players.
Warhammer 40,000 codex fluff has somewhat turned to this, YMMV of course. The most recent is the Grey Knights killing a coven of Sisters of Battle, then coating their armor in the latter's blood (something usually reserved for Khornate worshippers). This is in large part due to GW's new trend of Retconning old fluff rather than moving the plot forward. However, plotwise the fluff has already reached the literal last few minutes of the 41st millenium (the Medusa Campaign, taking place almost 5 real-life years ago, was said to have ended on the last year of the 41st millenium) and it would be hard to keep calling it "in the 41st millenium" when it's already 41,001, so it might be justified.
Similarly, many people took issue with a background event in the Blood Angels codex where the Blood Angels made a temporary alliance with the Necron army they were fighting to fend off a Tyranid assault. The Blood Angels then let the Necrons go as a Worthy Opponent (an OOC moment for both), foreshadowing the massive Retcon in Necron goals and philosophy (they used to be mindless killbots, now they're Tomb Kings IN SPACE!, and the fanbase continues debating whether or not this is a good thing).
This occurs sometimes in the shadowtalk sections of Shadowrun sourcebooks. It's somewhat inevitable, given the Loads and Loads of Characters featured in those sections (though the number of different characters has gone down in 4th Edition). The sourcebook Cyberpirates was especially bad for this, turning the poster Dr. Bones from a dwarf computer company CEO with a Star Trek-themed handle to an actual medical doctor who made excuses and defended the racist, experimenting-on-metahumans corporation that trained him. The poster Truthseeker was also altered from an anti-meta racist who thought there was a grand metahuman conspiracy to a pro-meta conspiracy theorist. Fortunately, the derailment of those two characters seemed to begin and end with that book.
The Legend of the Five Rings story has numerous examples, often as a result of the card game tournaments that guide the metaplot. Some examples:
Rokugan places high value on omens and portents, obtained from the mystical observations of the shugenja, and good or bad omens can shape public policy and major economic decisions. However, when the birth of Hantei XVI was presaged by horrible portents unseen since Iuchiban, all of the shugenja of Rokugan just decided to ignore the signs and let him take the throne anyway. Guess how that turned out.