Basically, differences in spelling, punctuation, etc. that aren't in spoken English.
There are some obvious homophones like its/it's and there/their.
I originally thought that the spellings of Kiev/Kyiv would fit, but I don't actually know if they have different pronunciations. The other example I thought of is weirder, and it's "trans woman" vs "transwoman". The former is seen as more trans friendly than the latter due to the word "trans" being used like other adjectives.
There are probably better examples out there.
Edit: There are also regional spelling differences like gray/grey and color/colour, but I don't think most of them have significant differences in meaning. (If you know some spellings that carry different connotations, I'd like to see them. I can't recall any at the moment.) I'd also associate regional spelling differences with accents (which are a part of spoken English).