Niantic Impactful Mistake Addition
An additional bug early in the game was that “fainted” Pokemon would return from gyms with 1 HP.
Revives had almost no use back then.
Edit: this is in response to the new guide released on this site. Points lost for not phrasing in the form of a question. DESPAIR.
Answers
I feel like there's gonna be a lot of suggestions about this. I'm surprised there wasn't the mention of Giratina-A being released with the wrong stats.
I think it's worth mentioning in the Espeon/Umbreon bit that the rates were fixed after some time but ended up getting reverted back to 0% before their career as raid bosses ended.
There was a pretty good bug in 2016-2017 that left certain specific gyms completely unplayable - network error if I recall. It started right after a CP change and went on for months.
There's currently a bug with certain pokemon from the CP rebalance that made the pokemon rewarded from archived research report the wrong CP. This was the same change that created eggs hatched partially healthy. It continues.
https://pokemongo.gamepress.gg/q-a/most-bizarre-glitch-ever
I think Niantic lacks in the QA department.