You have to force split into a list, before assigning it to the hash using square brackets . This discussed in this node about array and list context

>./test.pl some,kinda,sick,joke

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my @files=[
        {foo=>[qw/this that other/],
         bar=>[qw/them those they/]},
        {foo=>[qw/up down left right/],
         bar=>[qw/spin turn veer/]}
        ];

################# Square brackets round split ######
$files[2]{foo} = [ split(/,/,$ARGV[0]) ];

print Dumper @files;

__DATA__
$VAR1 = [
          {
            'foo' => [
                       'this',
                       'that',
                       'ottther'
                     ],
            'bar' => [
                       'them',
                       'those',
                       'they'
                     ]
          },
          {
            'foo' => [
                       'up',
                       'down',
                       'left',
                       'right'
                     ],
            'bar' => [
                       'spin',
                       'turn',
                       'veer'
                     ]
          }
        ];
$VAR2 = undef;
$VAR3 = {
          'foo' => [
                     'this',
                     'that',
                     'other'
                   ]
        };
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