I'm not sure if I can actually remember the 'first' one, but I can definitely remember the two biggest ones, and one of them was long enough ago that it might've been first but I don't recall.
Digimon season 2. Everything about that ending was horseshit. First off, the final villain is just Myotismon from season 1 again, which is seriously weak considering Myotismon wasn't even the biggest villain from season 1. Then his big villain plan is fairly non-threatening. And finally, they don't even beat him in a fight, they literally beat him with the power of positive thinking. Everybody thinks happy thoughts and it makes his body disintegrate. Like, wtf? That's bullshit. Even as a child I recognized that was utter bullshit. And then to add insult to injury, there's an epilogue after that where it shows all the characters in the future as adults, and none of their adult lives make any sense whatsoever, and frequently conflict with their personalities and character development throughout the show. Just... bullshit.
The other one that was definitely not first, but was pretty big was Batman: Arkham City. I've never been so disappointed by a game in my entire life, especially considering Arkham Asylum is one of my favourite games ever. Not only was Arkham City's gameplay not as good as I'd expected, but holy fuck that ending was garbage. The big villain plan that had been kept a super secret mystery all game and had been built up and hyped up all game was revealed and set in motion and... the entire plan is just for the army of military helicopters that have been flying around all game to start shooting at people. Just... what? Then it's all revealed to be a Ra's Al Ghul scheme, but it's not even a good Ra's scheme. Then he kills the main antagonist up to that point and then commits suicide in a mindbogglingly stupid way. THEN we get to a final, and fairly unnecessary confrontation with the Joker, except he's actually Clayface and that's our final boss. Clayface as the Joker's hired thug to pretend to be him. Weak. And THEN the actual ending has the Joker find a way to commit suicide that's somehow even more mindbogglingly stupid than Ra's and Batman cries over it. Also Batman is retarded and prioritized trying to save the Joker over trying to cure the thousands of people the Joker poisoned. And it's just... Even today I get absolutely fucking livid thinking about that game, and how the entire story was just such complete bullshit.