Lessons not teaching all listed words
Some of the lessons show a list of the words that you're supposed to learn, but then those words never come up. For instance, in Direction2, Lesson 1, じどうしゃ and アパート are listed, but don't appear with definitions. じどうしゃ shows up in a word bank once, but you never find out what it means unless it comes up in a practice session. This has happened on several other lessons as well.
Yep, I've had this issue too. In fact, on Dates, 3/5 only taught 1 out of 6 of the listed concepts. Not only that, but there were only two questions that asked basically the same exact thing. I've already finished Dates but 3/5's other 5 concepts still were not taught. This isn't completely hindering my learning, but it's definitely something that needs to be fixed.
That's true, there are some words listed as taught but they do not appear within the lesson, at least not at first. However, I noticed that if you redo the lesson after finishing it, you get different words and sentences. And while doing strenght exercises on a certain lesson, a bit more difficult tasks appear and almost surely the words listed as taught will be there.
For example, the "subculture" section (I know it's very far in the tree, but it's good for this example) has words like ninja, maid, otaku, cosplay. The lesson is very short and they weren't in there the first time I did the lesson, but some appeared while redoing it and with the strength exercise I got to learn them all. I hope that helps, revising is good not only for cementing knowledge, but also for getting new vocabulary :)