A few additional points:

• I notice that you want \| in your output. If you use qq|...| to quote the string you'll need to escape "\|" with "\\\|", not "\|". "\\" to escape the "\" and "\|" to escape the pipe.

  Alternatively, you could simplify matters and use a single quote syntax such as q{...} or any other delimiter that isn't in your string. \ will be taken literally, and the curly brace delimiters don't show up in your string so there is no need to escape the pipe or any other character.

• If you know that bad tags end in double square braces you can dispense with the negative lookahead  m{\[\[([^\[]+)\]\]}g The main thing to get rid of is that (.+) because "." matches everything including the end of tag character.

• When testing output via print statements, it is a good idea to put the delimiters front and back, just in case there is invisible whitespace at the beginning or end of your match, i.e. print "FOO:<$1>\n".

Revised code incorporating above points:

my $test = q{asdfas dfas dfas df asfd[[bad tag]] [[table]] asdfa sf as
+ [[asdf as f\|sfds]] as dfa 
sdf [[test new line]] foo};

while ($test =~ m{\[\[([^\[]+)\]\]}g) {
  print "FOO:<$1>\n";
}

#output - same as required in OP
FOO:<bad tag>
FOO:<table>
FOO:<asdf as f\|sfds>
FOO:<test new line>
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