(In case it wasn't clear, I was joking about the item names. I'm okay with the official names, but I do recognize that others consider the exact wording of these things to be quite important, even if it isn't something I get fired up about.)
Lines that didn't make sense in the official releases? In the annotated script I documented numerous examples, and I'm still only halfway through making notes on it. I certainly recommend reading it, because the details of the story make a great deal more sense when translated correctly, and in my notes I frequently explain how the internal logic of the story was distorted by previous translations. The problems go way
beyond whether Shadow would kill his mother or his best friend, or whether Sabin looks like a bear or a bodybuilder, or whether submarines exist in this world, or whether Imperial soldiers like watching Beavis and Butthead. Most of the problems are discussed by Mato in his video series, and some are additional observations I made. The annotated script can be read here: https://pastebin.com/RyVqkRnY
I'll talk about some examples that come to mind. Right from the beginning in the introductory text, the SNES version says that magic ceased to exist after the ancient war, but that isn't true: everyone who survived the war and knew how to use magic went into hiding. Magic still existed, but hidden away from people who wanted to exploit it. Later scenes reiterate the idea the Empire has found a way to create
magic power, when in fact all they've done is find where it already existed and harness it with their machines.
The scene near the beginning where Locke comes to help Terra escape is heavily mistranslated. The dialog makes it sound like Imperial troops are chasing her, and that Narshe is no match for the Empire, and they have to join the Returners to stay independent. What's really going on is that the Narshe guards are chasing her, and the city of Narshe does
have the strength to stand up to the Empire, but the people are too stubbornly independent to want to have anything to do with the Returners. The entirety of the exposition says the exact opposite of what it's supposed to say.
During the scene at the Returner base, both the SNES and GBA versions say that magical machines were used during the ancient war. The Japanese script says no such thing, and there nothing in the entire game to indicate that machines ever existed back then. Even the term "Magitek" itself is problematic, because it implies the connection of magic and technology, while the Japanese has no word like that anywhere. Consequently, both official translations end up saying 'Magitek' very frequently to describe magic usage, but the Japanese only ever uses more general terms for magic and rarely indicates a technological connection. It took me a little while to reconcile to this difference, but I ended up removing almost every instance of the term 'Magitek' from the script, and the only ones that remain are those that specifically refer to using magic and technology together.
Frequently the problems aren't easy to spot right away because they don't affect the entire scene, but certain lines within a conversation will say the wrong thing and end up skewing what is being talked about in a different direction. One example is when Banon is trying to persuade the Narshe elder to help the Returners. In the SNES version he says, "Our blood will spill because of you," but he's actually supposed to say, "We're asking you to shed blood." The original translation made it sound like he was saying the Returners would die because of the Narshe people, but that is nonsensical and doesn't fit the scenario. He's actually telling them that his request for them to join the Returners is a serious thing to consider, because he's asking them to kill for their cause.
Many people probably know about the mistranslated line that changed Setzer's entire character motivation, where the SNES version said the Empire had been good for his business, but he was supposed to say the opposite. What isn't as well known is that there are other examples of this same translation mistake in other places too, where certain NPC's say that their business is going up because the Imperial troops have left the area, but they're really supposed to be saying the Empire had been sustaining their business, and income has dried up once they left. Much of the NPC dialog throughout the game has issues of one kind or another: the entire section on the Imperial continent has a huge number of errors, and very few of the NPC's say what they are supposed to say during this part.
The subplot of Locke searching for the Phoenix Magicite to revive Rachel was particularly mangled. There was supposed to be a great deal of foreshadowing about this, but almost none of it survived into the SNES translation and it ends up coming out of nowhere late in the game as a result. Most of the references made by Locke (and NPC's talking about him) to searching for treasure are meant to refer to the Phoenix Magicite specifically, but it ended up just sounding like he wanted to plunder every place he went to get any old treasure.
The backstory of the Espers, both as related by Ramuh and in Terra's flashback, contained severe mistranslations which distorted the meaning of what was happening quite heavily. So many details were wrong there that I don't even have time at the moment to get into them, but all of them are covered in the annotated script. Celes' backstory as told by Cid also had a lot of mistakes: what he says about her childhood in Japanese is very different.
These are some notable examples off the top of my head, but there are many, many others scattered throughout. Some of them are subtle and some are not. I've spent a lot of time as an editor for a particularly prolific author friend, so over time I developed a keen sense for these kinds of issues with the internal logic of a story. So when I say this version captures the tone of the Japanese script, looking at it from a story editor's point of view is what I mean.
Now as to how noticeable these things are while actually playing the game? I'm not sure. For some this stuff may not matter much, if at all, but for others it's a bigger deal. I just found that I couldn't ignore the problems once I'd become aware of them. I'm actually really curious to hear about people's experiences of playing this version, and whether they find that their understanding of the story and sense of connection with the characters is affected in a meaningful way by the differences in how it is written.