$hash{entry} = "will get lost";
$hash{entry} = "this will replace it";
print $hash{entry};
[download]

die "Error: duplicate value for $key\n" if exists $hash{$key};
$hash{$key} = $value;
[download]

It's hard to say without an example of what the configuration file looks like, or how you've written the code that loads it. But my best guess is that whoever put in those new entries manually, introduced some syntax errors.

Assuming that your original configuration file looked something like this:

{
    cat => "meow",
    cow => "moo",
    dog => "woof"
}
[download]

{
    bird => "tweet"  # note missing comma
    cat => "meow",
    cow => "moo",
    dog => "woof"    # and here again
    pig => "oink"
}
[download]

Depending on how you loaded this hash (and the title of your post suggests that you use eval) then yeah, that could be the problem.

You may find it helpful to use something like YAML to load and save configuration information. It's not an immediate complete solution to your multiple entry problem, but consider the following:

use strict;
use warnings;
use YAML;
use Data::Dump;

my %configHash = (
    cat => 'Fred',
    dog => 'Joe',
);

my $cfgFileContents = YAML::Dump(\%configHash);

Data::Dump::dump (\%configHash);

print $cfgFileContents;
$cfgFileContents .= "cat: Bob\n"; # User added configuration entry

my $loaded = YAML::Load($cfgFileContents);

Data::Dump::dump ($loaded);

$cfgFileContents = <<DATA;
---
cat:
  - Fred
  - Bob
dog: Joe
DATA

$loaded = YAML::Load($cfgFileContents);

Data::Dump::dump ($loaded);
[download]

Prints:

{ cat => "Fred", dog => "Joe" }
---
cat: Fred
dog: Joe
{ cat => "Fred", dog => "Joe" }
{ cat => ["Fred", "Bob"], dog => "Joe" }
[download]

Note that the "User added configuration entry" gets lost (YAML specifies that there must be only one entry for each key in a hash and that additional entries will be ignored). However multiple values can be specified for a hash key if they are entries in a nested list, hence the nested array in the last line.