I wanted to complete this thread, to halp anyone, who might stumble into this...
To make sure ftrack understands files with different filenames AND different versions, we ended up manually naming the associated asset and omit the part where the files differ!
if we want to publish a file called "my_awsome_file_v001.jpg" and "my_awsome_file_v002.jpg", the created asset gets the name "my_awsome_file". So both files are linked to this asset, which make ftrack understand, that these are both just different versions of the 'same' file.
Thanks for your help