The Revit plugin calculates the model's building height using the difference between the lowest and highest elevation markers. Users can manually overwrite this export in the geometry page of the app, or with the most recent Revit Plugin update (v2.2.0) can change the building height before exporting. Read more about Building Height in an energy model here.
Solution: You have two options to fix this geometry input
>Option 1: Inside cove.tool, users can overwrite the plug-in generated values with a manual write-in input. This step will not overwrite the Daylight 3D Model Display, but will make the energy analysis model correct. Users can check their buildings actual height in the elevation or section view by using the measure tool in Revit to manually record their building's actual total height. This might be the ideal method if you do not return to Revit for a re-export.
>Option 2: Using the latest Plugin Update, version 2.2.0 released 04/10/2020 on the Autodesk app store, uses can alter the building height input manually before exporting into cove.tool.
Check how the plugin calculated building height
By opening an elevation or section view from your project browser, check that the Ground or Level 1 Level's Maker is at or near Elevation 0' 0". See image below to compare. In this case the project begins a 2'10" below project ground, but the occupied space begins at 5" above project ground. Exporting this buildings height would then be only 5" over your overall building height which shouldn't be a problem.