[2019] Trial by plague challenge not counting the missions correctly

What exactly do you mean? Are you talking about these?

It will record anytime you clear the map with that character class, at whatever difficulty you did it at. Having lvl 30 doesn’t mean you have cleared all the maps with that character class, as you could have done it on another class. For example, I was Kerillian lvl 200+ before I finally got around to clearing all maps on Legend with Shade. As I mostly played Waystalker.

Oh, they do. It didn’t count progress before they were introduced.

Smoker is correct. Most of the challenges weren’t retroactive when they were introduced back in June '18. Sorry for this.