SYMPTOM:
When trying to create a metric and switching to the subtotals tab in order to assign the available subtotals for the metric, Variance appears twice, as shown in the screenshot below:

CAUSE:
The Variance subtotal is a System Object and therefore, its ID is unified, which means it is the same across all the projects. Please refer to the following technical note for further information about the System Objects unification process:
KB34982 - New feature in MicroStrategy 9.0.2: Perform System Object ID Unification
In this particular instance, there are two subtotals with the same name because one of them has its ID unified whereas the other one doesn't. It is likely that the non-unified subtotal has been migrated with Object Manager from another project whose System Objects, or some of them, are not unified.