According to the bagit spec (v 0.97 and at least later versions of 0.96 if not all) the path provided in a fetch.txt file is relative to the base directory of the bag, not the data directory. The gem fetches relative to the data directory, e.g. a line in the fetch file like:
http://example.com/file.txt 1234 data/file.txt
winds up in data/data/file.txt instead of data/file.txt.