Some of these issues might be due to two things, which are a bit hard to explain. It's related to the manual font building in the final tab of the translation tools.
How they work is they go through all the translated texts that is flagged as the selected font, and compile a large list of what characters were used. They then build a font that has only these characters in it.
So, one possible reason for these issues is that I've accidentally called on the wrong font when rendering sometimes, like using BoldTitle instead of SmallTitle (not sure these are the actual names!)
If, in that case, the BoldTitle font does not contain the correct characters through a fluke, it doesn't know how to render the text properly, as the characters needed exists in the SmallTitle font.
Conversely, even if BoldTitle doesn't include a specific translated text, it might contain a lot of other texts that by chance includes some or all of the required characters. In that case the text can be rendered, but it's because of luck and nothing else. The more of the game that's translated, the bigger the risk/chance of this happening since there are a bigger set of glyphs in each font.
Another thing might be if you yourself forgot to remake the fonts after adding a bunch of new translations! It would almost seem that way in the specific case of the skill description, since it's so many different characters and none of them render as "?", but it could still be a fluke of course.
Solution on my end
One thing I might have to do is make it possible for a translated text to belong to more than one font, so I can use Label and SmallTitle for item names in different contexts, for example. This will require an update of the tools, but won't affect the translator's job very much!
At other places, there's probably bugs in the code, where I've simply used the wrong font for the job!