It has been going on for years. A character has a set origin that works, but for some reason latter writers come in and decide "well instead of that how about this?", and then the retcons commence. It seems to be much more a thing in the last 20 years than it was before with almost every character getting some new "tweak" to their origin. Sure some work out very well like Cap being frozen in ice or Magneto being the father of Quicksilver and the Scarlet Witch, but by and large most or not great and only hurt the character. So the question is which origin tweak hurt a character the most?
For me it is easy and that is Apocalypse. When he burst on the on scene he was quickly moved up to one of the top 3 X-Men villains alongside Sinister and Magneto. Then the retcons started. First the garbage 12 storyline were Apocalypse was reduced from and immortal bad ass to a parasite that has to jump from body to body. Then came the whole pawn of the Celestials thing from the Dark Angel Saga with the whole "death seed" thing. It seems like everytime they mess with him he gets worse and worse.