$temp =~ s/#$'//;
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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