There are some glyphs where a red x appears in places. What does this mean?
Have you accidentally activated the annotation tool?
If I have, I don’t know how I did it
Ah sorry, that is the result of one of the mekkablue scripts: https://github.com/mekkablue/Glyphs-Scripts/
In particular, Paths > Find Near Vertical Misses. it marks points that are just one or two units off the baseline, x-height, etc.
Technically these are glyph names. You can reset them with the Garbage Collection script.