Yes, some problems (On WAMP, PHP 5.3.0 ) with get_token_all() 

1 : bug line numbers
 Since PHP 5.2.2 token_get_all()  should return Line numbers in element 2..
.. but for instance (5.3.0 on WAMP), it work perfectly only with PHP code (not HMTL miwed), but if you have some T_INLINE_HTML detected by token_get_all() ,  sometimes you find wrongs line numbers  (return next line)... :(

2: bug warning message can impact loops
Warning with php code uncompleted (ex : php code line by line) :
for example if a comment tag is not closed  token_get_all()  can block loops on this  warning :
Warning: Unterminated comment starting line

This problem seem not occur in CLI mod (php command line), but only in web mod.

Waiting more stability, used token_get_all()  only on PHP code (not HMTL miwed) :
First extract entirely PHP code (with open et close php tag), 
Second use token_get_all()  on the pure PHP code.

3 : Why there not function to extract PHP code (to extract HTML, we have Tidy..)?

Waiting, I used a function :

The code at end this post :
http://www.developpez.net/forums/d786381/php/langage/
fonctions/analyser-fichier-php-token_get_all/

This function not support :
- Old notation :  "<?  ?>" and "<% %>"
- heredoc syntax 
- nowdoc syntax (since PHP 5.3.0)

I wanted to use the tokenizer functions to count source lines of code, including counting comments.  Attempting to do this with regular expressions does not work well because of situations where /* appears in a string, or other situations.  The token_get_all() function makes this task easy by detecting all the comments properly.  However, it does not tokenize newline characters.  I wrote the below set of functions to also tokenize newline characters as T_NEW_LINE.

<?php

define('T_NEW_LINE', -1);

function token_get_all_nl($source)
{
    $new_tokens = array();

    // Get the tokens
    $tokens = token_get_all($source);

    // Split newlines into their own tokens
    foreach ($tokens as $token)
    {
        $token_name = is_array($token) ? $token[0] : null;
        $token_data = is_array($token) ? $token[1] : $token;

        // Do not split encapsed strings or multiline comments
        if ($token_name == T_CONSTANT_ENCAPSED_STRING || substr($token_data, 0, 2) == '/*')
        {
            $new_tokens[] = array($token_name, $token_data);
            continue;
        }

        // Split the data up by newlines
        $split_data = preg_split('#(\r\n|\n)#', $token_data, -1, PREG_SPLIT_DELIM_CAPTURE | PREG_SPLIT_NO_EMPTY);

        foreach ($split_data as $data)
        {
            if ($data == "\r\n" || $data == "\n")
            {
                // This is a new line token
                $new_tokens[] = array(T_NEW_LINE, $data);
            }
            else
            {
                // Add the token under the original token name
                $new_tokens[] = is_array($token) ? array($token_name, $data) : $data;
            }
        }
    }

    return $new_tokens;
}

function token_name_nl($token)
{
    if ($token === T_NEW_LINE)
    {
        return 'T_NEW_LINE';
    }

    return token_name($token);
}

?>

Example usage:

<?php

$tokens = token_get_all_nl(file_get_contents('somecode.php'));

foreach ($tokens as $token)
{
    if (is_array($token))
    {
        echo (token_name_nl($token[0]) . ': "' . $token[1] . '"<br />');
    }
    else
    {
        echo ('"' . $token . '"<br />');
    }
}

?>

I'm sure you can figure out how to count the lines of code, and lines of comments with these functions.  This was a huge improvement on my previous attempt at counting lines of code with regular expressions.  I hope this helps someone, as many of the user contributed examples on this website have helped me in the past.

As a caution: when using TOKEN_PARSE with an invalid php-file, one can get an error like this:
Parse error: syntax error, unexpected '__construct' (T_STRING), expecting function (T_FUNCTION) or const (T_CONST) in  on line 15
Notice the missing filename as this function accepts a string, not a filename and thus has no idea of the latter.
However an exception would be more appreciated.

Not all tokens are returned as an array. The rule appears to be that if a token is not variable, but instead it is one particular constant string, it is returned as a string instead. You don't get a line number. This is the case for braces( "{", "}"), parentheses ("(", ")"), brackets ("[", "]"), comma (","), semi-colon (";"), and a whole slew of operator signs ("!", "=", "+", "*", "/", ".", "+=", ...).

The T_OPEN_TAG token will include the first trailing newline (\r, \n, or \r\n), tab (\t), or space. Any additional space after this token will be in a T_WHITESPACE token.

The T_CLOSE_TAG token will include the first trailing newline (\r, \n, or \r\n; as described here http://php.net/manual/en/language.basic-syntax.instruction-separation.php). Any additional space after this token will be in a T_INLINE_HTML token.

Well, there is a way to parse for errors. See
http://www.php.net/manual/function.php-check-syntax.php#77318