if ($temp =~ /#/){
        $temp =~ s/#$'//;
}
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That's what's causing the problem: $' can contain arbitrary data, but you try to treat it as a regex.

The "good" solution is to use this regex instead: $temp =~ s/#.*$//;

In general you can also quote interpolated variables, then they are treated as text, not as regexes:

my $varaible = '[a-z]';
m/\Q$variable\E/  # matches literal [a-z], not a character class.
[download]

If you're not inside a regex, quotemeta does the same job.