Incorrect vocabulary and leveling up progress

That’s correct. Using the default WaniKani settings, you’ll get all your previous level’s vocab before the new level’s content. You can change this to shuffled in the WaniKani settings if you want.

If you want even more flexibility, you can also check out [Userscript] WaniKani Lesson Filter, which would let you mix radical, kanji, and vocab lessons together in whatever combination you wanted.