The investigator can only, in this case, go by what shows up when they run their background check. It may, despite what you have still show that you were arrested or that you were “arrested and then it was downgraded.”
While I believe that you answered honestly, the record may show differently. I would start by checking with where the arrest occurred and see what they have. But, mistakes like this happen all of the time. Investigators and adjudicators see issues like this regularly.