From http://bugs.musicbrainz.org/ticket/3844

When "Move additional files" is checked, and e.g. *.jpg is moved, when files with the same name (e.g. front.jpg) from different folders is saved into the same folder only one is kept.

While I don't think that asking user really fits into the automated Picard flow, it could at least do the " (1)" trick, possibly, so people don't lose anything.