If a word is already in your vocab list (associated with another lesson) it is skipped instead of added to your vocab list a second time. The reason for this is because of the spaced repetition -- if someone knows a word we don't want to introduce it at the beginning of the queue again simply because it was added from a different lesson.
If you've had issues with other words not being added it is the first I've heard of the problem, but could always be an issue with the platform upgrade -- can you share more details on what words aren't getting added? Just an example so we can try to replicate.
In the meantime, if you just want to study lesson vocab, you can also go to the lesson page and then click on the vocab tab. The buttons that will appear in the left-hand column will let you launch the flashcards, review, etc. to study only the vocab associated with that lesson -- without the need for first adding it to your vocab list.