use strict;
use warnings;
my @content;
my @files;
my $dir;

my $input1 = "source/host1/";
my $input2 = "source/host2/";
my $name = "volume_2010_02";
#my $date = "2010-02-13";

opendir DIR1, "$input1";
my @files1= grep {$_ ne '.' && $_ ne '..' } readdir (DIR1);

@files = @files1;
#print @files,"\ninput file 1\n";

$dir = $input1;
#print $dir,"\ninput dir 1\n";
my @content1 = &readfiles(@files,$dir);
#print @content1,"\nFILE 1 Content\n\n";

@content =();
opendir DIR2, "$input1";
my @files2= grep {$_ ne '.' && $_ ne '..' } readdir (DIR2);

@files = @files2;
#print @files,"\ninput file 2\n";

$dir = $input2;
#print $dir,"\ninput dir 2\n";

my @content2 = &readfiles(@files,$dir);
#print @content2,"\nFILE 2 Content\n\n";
push @content1,@content2;
my @file = sort {$a cmp $b} @content1;
print @file,"\nPush output\n\n";
my %output;
my $print;
my $semiprint;
foreach(@file)
{
    #print $_,"\nCOntent1\n\n";
    my ($key,$val) = split (/\,/,$_);
    $semiprint .= "$key,$val\n";
    #print $semiprint,"\nsemi in loop\n\n";
    $output{$key} += $val;
    $print .="$key,$output{$key}\n";
    #print $print,"\nFinal output\n\n";
}
#print $print,"\nFinal output\n\n";
#print $semiprint,"\nsemi output\n\n";
open OUTPUT, "> target/1.dat";
print OUTPUT $print;

sub readfiles
{
    my @file = @files;
    my $directory = $dir;
    
    foreach(@file)
    {
        #print $_,"\nFILE NAME\n";
        if($_ =~ /^$name/)
        {
            #print $_,"\nFile found \n";
            open FILE,"< $dir/$_";
            while(<FILE>)
            {
                chomp;
                push @content,$_;
            }
            
        }
    }
    return @content;
}
[download]

__CONTENT FILE 1__
2010-02-12_aaa,654
2010-02-12_bbb,374
2010-02-12_ccc,158
2010-02-13_aaa,745
2010-02-13_bbb,786
2010-02-13_ddd,852
2010-02-14_bbb,754
2010-02-14_aaa,169
2010-02-14_ccc,965
[download]

__CONTENT FILE 2__
2010-02-12_aaa,654
2010-02-12_bbb,374
2010-02-12_ccc,158
2010-02-13_aaa,745
2010-02-13_bbb,786
2010-02-13_ddd,852
2010-02-14_bbb,754
2010-02-14_aaa,169
2010-02-14_ccc,965
[download]

__OUTPUT__
2010-02-12_aaa,654
2010-02-12_aaa,1308
2010-02-12_bbb,374
2010-02-12_bbb,748
2010-02-12_ccc,158
2010-02-12_ccc,316
2010-02-13_aaa,745
2010-02-13_aaa,1490
2010-02-13_bbb,786
2010-02-13_bbb,1572
2010-02-13_ddd,852
2010-02-13_ddd,1704
2010-02-14_aaa,169
2010-02-14_aaa,338
2010-02-14_bbb,754
2010-02-14_bbb,1508
2010-02-14_ccc,965
2010-02-14_ccc,1930
[download]

__EXPECTED OUTPUT__
2010-02-12_aaa,1308
2010-02-12_bbb,748
2010-02-12_ccc,316
2010-02-13_aaa,1490
2010-02-13_bbb,1572
2010-02-13_ddd,1704
2010-02-14_aaa,338
2010-02-14_bbb,1508
2010-02-14_ccc,1930
[download]

You can't build your output string until you've processed all the entries in your files. Replace the print just before your subroutine with

print OUTPUT "$_,$output{$_}\n" for sort keys %output;
[download]

Your file will now contain:

2010-02-12_aaa,1308
2010-02-12_bbb,748
2010-02-12_ccc,316
2010-02-13_aaa,1490
2010-02-13_bbb,1572
2010-02-13_ddd,1704
2010-02-14_aaa,338
2010-02-14_bbb,1508
2010-02-14_ccc,1930
[download]

Your next task is to tidy up your source code, it's a mess :-)

Some hints:

• You use strict and warnings. This is very good.
• Always check that your opens and opendirs succeeded.
• Don't call subroutines using &readfiles(...). You don't need the "&" and it doesn't do what you think it does.
• Pick more meaningful variable names, @files and @files2 are rarely good choices.
• You don't seem to understand the point of calling subroutines with parameters. See perlsub.
• Always declare variables in the smallest possible scope. Coping with Scoping may help (its old, but still worth a read).
• Most importantly, enjoy your Perl programming.