Hi,
apt-file is not able to find files provided by the alternative system. I understand that those files are not exactly "a file in the package" but the package is reponsible for the file being there and therefore apt-file should find it.
I stumbled upon that when searching for packages that provide /usr/bin/mail. Both apt-file and packages.debian.org only find the package 'mailutils' but IIRC there are at least 3 other packages which provide it via the alternatives system, bsd-mailx for example.
I was unsure of the priority of this bug. On the one hand i'd say it's a wish, on the other hand i think this tool is pretty useless if it's just going to ignore things like alternatives and who knows what else might come altogether and just displays a minor subset of relevant packages.
Thank you and best regards
Hendrik