The only time this has come up previously was several years ago but it involved Final Cut Pro 6 and XDCAM Transfer 2.7. There was no mention from anyone about trouble with Premiere Pro and of course Sony Content Browser was several years away from being released. It turned out to be a bug in Final Cut Pro that was solved with updates to the program.
There was talk that if XDCAM EX files were imported into an existing project that duplicate filenames would appear but if the clips were imported into a new project the problem disappeared. Sony did come out with another program called Sony Log and Transfer that allowed the importing of XDCAM files from within Final Cut Pro and that also made a difference.
I don't know if any of this info is going to be relevant to your situation but at least you know now that you were not the only one with this issue. For more info on this just do a search in this forum using the "duplicate clips" or "duplicate filenames" search terms.You'll find stuff from as far back as 7 years ago.