If you have added %phone to your "New Ticket Alert" then you will need to change the file ./include/class.ticket.php in order for this to work.
You will need to add the following line around line 990:
$body = str_replace("%phone", $ticket->getPhone(),$body);
It's near the line:
//If enabled...send alert to staff (New Ticket Alert)
a little bit below here there are some $body = str_replace() lines, just add the above one between them.
Off course this is only for the New Ticket Alert.