There is currently a bug in the Accounts Imports when the 'Create New' option is not enabled when mapping Structure fields.
When this checkbox is not ticked, Accounts will be assigned to all structure groups with the same name.
If you have a structure with the top level 'Country' and the second level 'Store Type', if you have the same Store Types in each Country, no matter how accounts are mapped, they will be assigned to all Store Types with the same name.
To avoid an Account being assigned to multiple structure groups, we recommend enabling the 'Create New' function when importing.
During the Field Mapping stage of an Account Import, make sure to tick the Create New option for all structures.