I don't understand your question. Does an excel have several columns with the same name? Or do you have excel files that by themselves each have unique field names, but they have some field names in common with some of the other excel files? This first cannot be handled other than renaming field names (or Qlikview will do it for you). The other can be handled by forcing the data to be concatenated into one table using the CONCATENATE directive.
LOAD A, B, C, D FROM excelfile1 (ooxml, embedded labels, table is Sheet1);
LOAD A, B, F, G FROM excelfile2 (ooxml, embedded labels, table is Sheet1);
I faced a similar issue and was able to get around but in my case they did not need to be related and was mostly data from different years that I wanted to compare. It will also rename the columns for your tables.
This is what worked for me.
Open your Qlik App, go to Data Manager, Click Add Data, (add you first table as you would normally do).
Then while still being in Data Manager, Click Add Data, choose your second table. Prior to Clicking on load and finish, there is a Profile button. Click on Profile button and onto you should see under Recommendation, No Association button.
Select No Association button, and click Rename Fields. Then go ahead a load the data.
You should be able to load the two table, but then again this is may not be what you are looking for.