use Data::Dumper;
print Dumper(\%ini)."\n";
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And you have two typos:

        push @slots, keys%{$ini{'$hostnames[$i}'}};
        push @ifindices, values%{$ini{'$hostnames[$i}'}};
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Please remember, that keys() and values() don't return the same order of items, so you won't get any associations between slots and ifindices. Try

for (keys(%{$ini{$hostnames[$i]}})) {
 push @slots,$_;
 push @ifindices,${$ini{$hostnames[$i]}}{$_};
}
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Last note:
If you don't really need $i, you could advoid it:

for (@hostnames) { print $_; }
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for my $Hostname (@hostnames) { print $Hostname; }
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this:

for (keys(%{$ini{$hostnames[$i]}})) {
 push @slots,$_;
 push @ifindices,${$ini{$hostnames[$i]}}{$_};
}
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how can I use it? $i is the variable inside the for loop (my $i). What I am trying to do is:

to associate slots with indices for every host (performance section, pop1 & pop2). The simplest way I thought was with an ini file (since I have worked before with ini files.)

Thanks!

$_ ist the default variable for loops, you don't need a special inside variable.
If you got such a loop (and don't see any commands that could harm your computer), it's wise to

for (keys(%{$ini{$hostnames[$i]}})) {
 print "Slot: $_\n";
 push @slots,$_;
 print "IfIndex: ${$ini{$hostnames[$i]}}{$_}\n";
 push @ifindices,${$ini{$hostnames[$i]}}{$_};
}
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This will show you what is happening.

Let's split the lines: $hostname[$i] contains your hostname. This is used as a key for the %ini - hash. So we could simplify it for better understanding as

for (keys(%{$Hostpart_from_INI})) {
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$Hostpart_from_INI contains a reference to what Config::INI found for this hostname (the one for the current loop run). It is a Hash-Reference, so we could also write:

for (keys(%Host_Data_from_INI)) {
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Okay, now we're here with a simple Hash. Each loop run gets another key from the Hash %Host_Data_from_INI. If you got Problems with $_, we could add it:

for $_ (keys(%Host_Data_from_INI)) {
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You should try the following for better understanding:

perl -le 'for (1,2,3) { print $_; }'
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You could also add the $_ behind the for or you could use any other variable.
Still with me? Okay, let's write your loop using the simplified form:

for (keys(%Host_Data_from_INI)) {
 push @slots,$_;
 push @ifindices,$Host_Data_from_INI{$_};
}
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Remember: We changed nothing, the code is still the same. All we did was renaming things and solving references to show what Perl sees when executing the script.

I get: 2 4 instead of 2 2 4

A hash never has duplicate keys. Your ini file sets the same parameter twice: one setting overrides the other. After all, there are only two parameters in the [pop1] section: 2 and 4. So you get exactly what you set in the ini: two keys.

you forgot my $i, or is $i another global? Use strict warnings and diagnostics or die

Yes I forgot my $i. Now the syntax of the code is correct. What I want to do is to be able to assosiate slots with indices for every host using ini file format. Can you help me please, cause I am new to perl...

Don't struggle with ini, use YAML

#!/usr/bin/perl --

use strict;
use warnings;

use YAML;
use Data::Dumper;

sub printdump {
    print Dump($_[0]),"\n\n";
    print Data::Dumper->new([$_[0]])->Indent(1)->Dump,"\n";
    print "---------- $_[0] ----------\n";
}

{
    my %ini;    
    $ini{performance}{pop1}{ip}  = q{192.168.1.1};
    $ini{performance}{pop1}{slots} = [
            {2 =>  123},
            {2 =>  345},
            {4 =>  125},
    ];
    $ini{performance}{pop2}  = {};
    $ini{performance}{pop2}{ip}  = q{192.168.1.2};
    $ini{performance}{pop2}{slots} = [
            {6 =>  503},
            {10 =>  444},
    ];
    printdump(\%ini);
}


{
    my %ini;
    $ini{performance}{pop1}=[
        q{192.168.1.1},
        {2 =>  123},
        {2 =>  345},
        {4 =>  125},
    ];
    $ini{performance}{pop2} = [
        q{192.168.1.2},
        {6 =>  503},
        {10 =>  444},
    ];
    printdump(\%ini);
}

{
    my %ini;
    $ini{performance}{pop1}=[
        q{192.168.1.1},
        [2 =>  123],
        [2 =>  345],
        [4 =>  125],
    ];
    $ini{performance}{pop2} = [
        q{192.168.1.2},
        [6 =>  503],
        [10 =>  444],
    ];
    printdump(\%ini);    
}


{
    my %ini;
    $ini{performance}{pop1} = [qw[
        192.168.1.1
        2    123
        2    345
        4    125
    ]];


    $ini{performance}{pop2} = [qw[
        192.168.1.2
        6    503
        10   444 
    ]];
    printdump(\%ini);    
}


{
    my %ini;
    $ini{pop1} = [qw[
        192.168.1.1
        2    123
        2    345
        4    125
    ]];


    $ini{pop2} = [qw[
        192.168.1.2
        6    503
        10   444 
    ]];
    printdump(\%ini);    
}
__END__
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Read more... (3 kB)
or even JSON

He is already using Config::IniFiles. The other config modules are all very similar, syntax varies slightly (ex heredoc support), most don't support duplicates, and they all have various other quirks (and bugs).

YAML is much better alternative .

If you have to use ini, I strongly recommend Alias' Config::Tiny http://search.cpan.org/~adamk/Config-Tiny-2.12/lib/Config/Tiny.pm