BEIC upload policy implies Commons upload of two files per book - an original pdf and a derived djvu with the same file name, the extension only being obviously different; the djvu file comes from an upload of pdf file into IA too, then runnin IA Upload tool.
When we tried to upload File:Buonarroti, Michelangelo – Rime, 1960 – BEIC 1775670.djvu and File:Boiardo, Matteo Maria – Opere volgari, 1962 – BEIC 1773914.djvu, IA Upload tool silently failed; on the contrary, IA Upload successfully uploaded the same files named as File:Buonarroti - Rime.djvu and File:Boiardo - Opere volgari.djvu (then renamed into Commons from a rename request; see file chronology).
I found that Commons throws a warning after a try to upload files when a file with a very similar file exists; I presume that IA Upload tool could be confused by that warning.