BlindElephant attempts to detect and ignore custom 404 pages, but this is not always effective and has the result of occasionally producing "Retrieved file doesn't match known fingerprint" results for a file when the content from the remote host is actually completely bogus. When scanning massive numbers of hosts with guess-apps this produces many false positives, and so during app guessing indicator files that don't match known fingerprint are considered non-existent (eg, during app guessing, BlindElephant prefers FN over FP).
This behavior is not always suitable, and should be configurable via a parameter to WebAppFingerprinter.guess() and the command line.
(This also contributes to some of the problems in bug 3059047, "Foreign langauge versions of some apps cause detection issue" https://sourceforge.net/tracker/?func=detail&aid=3059047&group_id=330762&atid=1387418 )