The formula uses Issue property Issue status that works on individual issues only.
eazyBI uses an optimization for total calculation. It executes the same formula on totaling row independently from the report results. The validation for issue status = Done fails for totaling row, and it picks up remaining estimated hours as the status is empty (not Done) for totaling row.
I updated the formula, to get it working on issues only. It will check if there is any value in status at all and only then look for a particular status value. This will force to sum up value in columns for total calculation.
not isempty([Measures].[Issue status])
0-[Measures].[excess hours / hours left over],
[Measures].[Remaining estimated hours])