I came with the problem when exit from the vim with “:q” command.

NERDTree still display after :q command

and this seems the buffer window counter problem.

fix by:

function! CheckLeftBuffers()
  if tabpagenr('$') == 1
    let i = 1
    while i <= winnr('$')
      if getbufvar(winbufnr(i), '&buftype') == 'help' ||
          \ getbufvar(winbufnr(i), '&buftype') == 'quickfix' ||
          \ exists('t:NERDTreeBufName') &&
          \   bufname(winbufnr(i)) == t:NERDTreeBufName ||
          \ bufname(winbufnr(i)) == '__Tag_List__'
        let i += 1
      else
        break
      endif
    endwhile
    if i == winnr('$') + 1
      qall
    endif
    unlet i
  endif
endfunction
autocmd BufEnter * call CheckLeftBuffers()

https://yous.be/2014/11/30/automatically-quit-vim-if-actual-files-are-closed