Did you use the Workspace Debugger to get the API call?
Workspace reports use API 2.0 to pull the data, so there should be no reason for the data to be different, unless the API call has some minor logic differences that could be causing a slight variation.....
To see the API calls for your Workspace Reports, turn on Debugging from the Help Menu (this will add a new bug icon to your visualizations)
Click on this icon, and it will first ask you if you want the Freeform Table or Sparkline, choose the Table. Then it will show you timestamps of the APIs... keep in mind that complex data pulls could be using multiple requests.
When you click on the timestamps, a new page will open showing the API call in multiple formats.
I would compare your API requests for differences, this is the most likely cause of the discrepency.