When calculating structure factors from a structure, VESTA always seems to access the element, instead of the ion defined by the charge state. Tested for several elements on Versions 3.5.8 and 3.90.5a. This may be caused by the database entry e.g. O2-, whereas in the charge box it has to be -2, but changing the database entry to O-2 does not fix the access.
The workaround I've found is not pretty, but you can just change the database file entry for the element to match that of the ion you want to access. I recommend making a backup copy of the 'asfdc' file before changing any entries.
Best, LC