I had this happen on a PS4 save. I walked into the museum and counted everything on the display tables, then counted the number of mineral & artifacts in my journal. It was off by one. I looked at each row in the journal and visually located each item in the museum until I found a mineral I had apparently failed to donate. I'd found two of them, according to the journal, but I must have mistaken it for a similar looking mineral. I had to crack open a lot of geodes to find a third and donate it. ^_^