To determine where the problem is:
Make the necessary report selections within the QVW and the do 'send to excel' by right-clicking on the chart and selecting 'send to excel' from the context menu.
Do you get the same unexpected results when exporting to excel from the QV desktop?
If the issue occurs using send to excel, then the issue is actually with QV desktop itself.
In any case, in order to perform a more detailed investigation, please report the issue to the Qlik Support Desk at the link below.
If you do not have access to the Qlik Support Desk, please contact firstname.lastname@example.org in order to provide you with access credentials.