I have encountered this problem too. And it is barely documented this one comes pretty close to how I could describe the problem.
The problem is either :
a) apt (client) cannot handle packages on a vhost.
b) apt (client) has a problem with the symlinks
I haven't tested it much further yet to find out wich one is exactly causing the problem but this is how I solved it :
RedirectMatch ^/$ /apache2-default/
# RedirectMatch ^/$ /apache2-default/
As a mirror takes quiet a bit of space and is something you don't want to lose then its a good idea to have it on a seperate partition or even disk.
chown apt-mirror /var/www/repositories
mount /dev/[your mirror disk] /var/www/repositories
for future use :
# set base_path /var/spool/....
on line :7
set base_path /var/www/repositories/
when finished restart your webserver
Now change your clients sources list to search the new path.
As said : this way does probably more then is needed to fix the problem feel free to test it partitial and reply the method that does it alone
I also know that I'm a bit late with respons but I had this problem now and this forum came close to my search string so it will be usefull for others too.