You might want to try declaring @uploads outside the scope of the foreach loop, i.e.

sub getfiles()
{
  opendir DIR,$logSite or die "Unable to open Directory, please try ag
+ain";
  my @uploads;
  foreach $pattern (@ARGV)
  {
    push (@uploads, grep /$pattern/, readdir(DIR));
  }
  closedir DIR;
   
  return \@uploads;
}
[download]

Using strictures (use warnings; use strict;) would've helped enormously.