Yes, this is expected, though not necessarily ideal. When you're using the live connection to Excel, Tableau "knows" what you are connecting to and creates the hierarchical grouping by source table in the Dimensions and Measures windows. When you're using the extract, Tableau has "flattened" your data and does not show that source table information.
As for the duplicate rows, to avoid them you need to be careful with how the join(s) between the tables is/are defined, and possibly use Custom SQL. Sometimes there is no way around duplicate rows and you have to do some filtering within Tableau. I can't say more without seeing how your data is laid out, if you post a packaged workbook with some sample data someone here on the forums could help you out.