Perhaps the value doesn't end in a newline, or perhaps someone changed $/. You can check what the values of $line and $/ using

use Data:::Dumper;

{
   local $Data::Dumper::Useqq = 1;
   print(Dumper($var));
}
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You might have better luck with the following:

$line =~ s/\s+\z//;
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It removes all forms of whitespace from the end of the line (except NBSP U+00A0 in some circumstances).