Hi there, and thanks for voicing your concerns!
Actually we have had this kind of thread posted a couple of times recently, so I thought I would address it here. When the vocab lists were first made (specifically the N-level ones, not the A-lists), we compiled several of the most common and reliable textbooks available, in addition to vocab lists that were available online.
We found that these textbooks usually had double-ups when it came to grammar and vocabulary between their respective grammar and vocabulary textbooks as well. As an example, I have taken some screenshots here from the N3 Shinkanzen Master Vocab textbook, illustrating their duplication of what would also be considered grammar.
(Note that I just gave these a quick glance over, so I may have missed a few)
If I had to hazard a guess at why this is done on the whole between teaching resources, my guess would be that it is because textbooks tend to have comparative or word family based segments. So basically they are listing sets of words together and often making comparisons between them specifically for the purpose of showing differences in usages and similarities.
As Bunpro doesn’t specifically do this in our vocab decks, and presents them purely as ‘lists’, that nuance can be lost and it can feel a bit like ‘why is this in both sections of the site’, despite that being quite normal across the board in textbooks. We may do something like this in the future, and actually have done it for our revised version of N5 which we have divided into logical sets of words. This revised version of N5 will be released quite soon.
As for your specific level-related observation, I would say this is primarily just a failure of stricter content control on our part, where one book had something at one level and another had it at another level, then when we added it, we added them to one specific deck without giving this the particular attention that it perhaps deserved. To be perfectly honest, we haven’t decided what we are going to do with these double-ups across both vocab and grammar yet, but at the bare minimum, I agree that ensuring that they are taught at the same level will lessen the confusion.