I uploaded small set of files to Commons. For some reason GWToolset named all those as "Array.jpg"
https://commons.wikimedia.org/wiki/File:Array.jpg
As you can see from the history, GWToolset uploaded all images over the previous image with the name "Array.jpg"

Here is the XML I used:
http://opendimension.org/misc/kiasma_set2.xml

I used this mapping (*except* that I used "title" in XML for "gwtoolset title"):
https://commons.wikimedia.org/wiki/GWToolset:Metadata_Mappings/Artturimatias/Flickr2GWToolset-photo.json

I also tested with Beta with the same file. It also resulted Array.jpg, but not image overwrites (no history).
http://commons.wikimedia.beta.wmflabs.org/wiki/File:Array.jpg

I uploaded files from same set successfully yesterday (23rd). The only difference that I can think of is that the failed upload had a language attribute in the title and the successful didn't.