Missing a end bracket. Also you could make this better like:

on *:text:*:#: {
  if ($1 == !start) {
    if (!%startctime) {
      msg $chan Counter has initiated
      set %startctime $ctime
    }
    else {
      msg $chan Counter has already started
    }
  else if ($1 == !stop) {
    if (%startctime) {
      msg $chan Timer has been stopped at 12 $calc(%endctime - %startctime) Seconds
      msg $chan Or $duration($calc($ctime - %startctime))
      unset %startctime
    else {
      msg $chan Counter hasn't been started
    }
  else if ($1 == !info) {
    msg $chan This bot was created by Carlosrevilla and shared to the Hawkee community
  }
}

set %startctime 0
set %endctime 0

It's better to use unset %startctime and just delete the variable.