The entries were probably not dropped, but overwritten:

$hash{entry} = "will get lost";
$hash{entry} = "this will replace it";
print $hash{entry};
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In order to catch the error, you need to change the code that loads the values. Instead of $hash{$key} = $value you might use

die "Error: duplicate value for $key\n" if exists $hash{$key};
$hash{$key} = $value;
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See also perldata, or even perldsc on how to store several values at the same key.