Square Enix has been doing this with some of their PS1 RPGs conversions recently. It usually falls under one of two changes:
Certain lines of dialogue are made gender neutral (e.g. references to a character being called “ladylike” are replaced with neutral alternatives)
Fanservice has been toned down (iirc a character in Chrono Cross has had her outfit altered to be less risqué)
These sorts of cuts have, unsurprisingly, proven to be quite divisive. Square should probably have included a classic mode to present the games as they were made in the late 90s, which would satisfy purists who want the original titles, warts and all. The framing of a classic mode would also help keep expectations in check.
Found another one while looking up info about The Combatribes.
The SNES version was slightly altered for its Virtual Console re-release: the bad guys’ organisation was changed from “Ground Zero” to “Guilty Zero”, presumably because of 9/11 and the fact the game takes place in New York City.
Like the Arcade1Up cabinet before it, the theme song of the first Teenage Mutant Ninja Turtles arcade game is replaced with a cover version in the Cowabunga Collection.
Arcade
Cowabunga Collection
Also, the Pizza Hut logos are removed from Teenage Mutant Ninja Turtles II: The Arcade Game (NES).