There is one thing you may ask those Revit guys to try.
In Revit Stories are defined by Level objects. These Level objects are placed in Sections or Elevations and they can be set to define a Building Story.
Select a Level object in Revit and check its "Building Story" property. If it is checked, the Level defines a Building Story.
Maybe they should check whether this property is set correctly for all their Levels defined in the Revit file so it is checked only for those Levels that are actual Stories of the Building.
Also, I think they should check if all their objects are constrained to these Building Story Levels, an not to any other auxiliary Levels they might have defined in their file.
This may clean up thing a bit.
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