They also have interlaced two seasons of some shows together (noticed this on a couple kids shows for my daughter). So it would go season 2 ep 1, season 3 ep 1, 2-2, 3-2, etc. In general it wouldn't matter for a kids show that doesn't have a continual storyline, but when you only pay for season 2, it then stops at the end of each episode instead of continuing on automatically, and you have to go back to the UI and skip one.
That 'feature' of Amazon's service really annoys me as well - presumably it's to make it look like they have far more content available than they actually have?
I don't know where you are but Netflix streaming in the U.S. has the first three seasons of "Lucifer" as well as the 4th season sold directly to Netflix.
Similar gripe, finding out that only the sequel or the last movie in a trilogy is available: why Netflix, why?