(Similar to bug 67144)
I have just completed the upload of an XML with 3018 records. I can see 2977 files in my tracking category. What happened to the dfference? No idea. I suppose they were skipped as already present on Wikimedia Commons but I have no idea. Now I have to reindex all files uploaded to try to figure it out.
Would be nice if GWToolset would have written a log/report somewhere, eg in one of my subpage, of what happened.