I'm confused. Cutting and pasting your code and using a zip and a zip.meta file, neither file matches both regexes:

my @uploads = qw(foo.zip bar.zip.meta);
foreach my $count (0, 1) {
if($uploads[$count] =~ m/zip$/i)
           #/.*(zip)/
        {
            print "I GOT A ZIP\n";
        }else{
            print "I got NADA\n"
        }

        if($uploads[$count] =~ /.*(meta)/){
            print "I GOT A META\n"
        }else{
            print "I got NADA\n"
        }
}

__END__
I GOT A ZIP
I got NADA
I got NADA
I GOT A META
[download]

So, what's your real problem?