Final Fantasy Type-0
Translation that competed with an official localization, that had a lot of hostility against it from game journalists and some audiences, leading to its Achilles' heel being quickly exposed - the team lead was maintaining many patches on the same blog that convert multi-disc PSP games by Square Enix to a single UMD ISO, Final Fantasy Type-0 included, and as it turns out that included significant prepatched portions in the patch data.
Then one of the haters programmed a tool that converts the translation patch to a working ISO (the patch used to require the legally ripped UMD image), and then urged Square Enix to act against this ongoing "piracy".
As for the other Chrono Trigger related patches, it was collateral damage from a site takedown aimed at the 3D remake. Which began as a fan game, but then the fangame developer went to E3 and started asking around other Western publishers to publish the remake. Square Enix certainly disagreed with the notion that it's abandonware, and the rest is well documented.