$temp =~ s/#$'//; I'm not even sure what you want that to do, but it constructs a regex out of # followed by whatever was followed by the previous match. Any regex special characters in that generated string will be interpreted as regex directives.

You probably want something like:

while (chomp(my $temp=<INPUT>)){
    print Dumper $temp;
    $temp =~ s/#.*//;  # remove comments
    if ($temp =~ /^\s*$/){
        next;
    }
    print "after regex:\n";
    print Dumper $temp;
    print "end\n";
}
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