The issue is found in:
https://github.com/joaotavora/yasnippet/issues/761#issuecomment-270693995

On Fri, Jan 6, 2017 at 10:29 PM, Jiajian Huang <ispinfx@gmail.com> wrote:

> Remember to cover the basics, that is, what you expected to happen and
> what in fact did happen.  You don't know how to make a good report?  See
>
>      http://orgmode.org/manual/Feedback.html#Feedback
>
> Your bug report will be posted to the Org mailing list.
> ------------------------------------------------------------------------
> Bug(maybe): org-edit-special under org 9.x does not preserve the leading
> spaces in black line or dose not indent the blank line after exit editing.
>
>
> Reproduce steps:
>
> Launch emacs by `emacs -Q`, eval the following snippet(assumed org 9.x
> is installed via elpa)
>
>     (package-initialize)
>     (require 'org)
>
> open a org buffer, input the source by <s and type `python`
>
> #+BEGIN_SRC python
>
> #+END_SRC
>
> use C-c ' to edit the block and input
>
>     for i in range(10):      # input this line and <enter>
>         # there are 4 spaces before the '#' now
>
> use C-c ' to close the source block buffer and back to org-mode, we can
> see the first line of the block is indented 2 spaces by org while the
> blank line
> isn't.
>
>
> ​
>
> Emacs  : GNU Emacs 25.1.1 (x86_64-apple-darwin16.3.0, Carbon Version 157
> AppKit 1504.76)
>  of 2016-12-23
> Package: Org mode version 9.0.3 (9.0.3-elpa @
> /Users/Yomisuko/.emacs.d/elpa/org-20161224/)
>
> current state:
> ==============
> (setq
>  org-tab-first-hook '(org-babel-hide-result-toggle-maybe
> org-babel-header-arg-expand)
>  org-speed-command-hook '(org-speed-command-default-hook
> org-babel-speed-command-hook)
>  org-occur-hook '(org-first-headline-recenter)
>  org-metaup-hook '(org-babel-load-in-session-maybe)
>  org-confirm-shell-link-function 'yes-or-no-p
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  org-src-mode-hook '(org-src-babel-configure-edit-buffer
>     org-src-mode-configure-edit-buffer)
>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>  org-babel-pre-tangle-hook '(save-buffer)
>  org-mode-hook '((closure
>  (org-inlinetask-min-level buffer-face-mode-face org-mode-map
>   org-tbl-menu org-org-menu org-struct-menu org-entities
>   org-last-state org-id-track-globally org-clock-start-time
>   texmathp-why remember-data-file
>   org-agenda-tags-todo-honor-ignore-options iswitchb-temp-buflist
>   calc-embedded-open-mode calc-embedded-open-formula
>   calc-embedded-close-formula align-mode-rules-list
>   org-emphasis-alist org-emphasis-regexp-components
>   org-export-registered-backends org-modules
>   org-babel-load-languages t)
>  nil
>  (add-hook (quote change-major-mode-hook) (quote org-show-block-all)
>   (quote append) (quote local))
>  )
> #[0 "\300\301\302\303\304$\207"
>   [add-hook change-major-mode-hook org-babel-show-result-all append
>    local]
>   5]
> org-babel-result-hide-spec org-babel-hide-all-hashes)
>  org-archive-hook '(org-attach-archive-delete-maybe)
>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
>  org-cycle-show-empty-lines
>  org-optimize-window-after-visibility-change)
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-link-parameters '(("id" :follow org-id-open)
>       ("rmail" :follow org-rmail-open :store org-rmail-store-link)
>       ("mhe" :follow org-mhe-open :store org-mhe-store-link)
>       ("irc" :follow org-irc-visit :store org-irc-store-link)
>       ("info" :follow org-info-open :export org-info-export :store
> org-info-store-link)
>       ("gnus" :follow org-gnus-open :store org-gnus-store-link)
>       ("docview" :follow org-docview-open :export org-docview-export
> :store org-docview-store-link)
>       ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
>       ("bbdb" :follow org-bbdb-open :export org-bbdb-export
> :complete org-bbdb-complete-link :store org-bbdb-store-link)
>       ("w3m" :store org-w3m-store-link) ("file+sys") ("file+emacs")
>       ("doi" :follow org--open-doi-link)
>       ("elisp" :follow org--open-elisp-link)
>       ("file" :complete org-file-complete-link)
>       ("ftp" :follow
> (lambda (path) (browse-url (concat "ftp:" path))))
>       ("help" :follow org--open-help-link)
>       ("http" :follow
> (lambda (path) (browse-url (concat "http:" path))))
>       ("https" :follow
> (lambda (path) (browse-url (concat "https:" path))))
>       ("mailto" :follow
> (lambda (path) (browse-url (concat "mailto:" path))))
>       ("message" :follow
> (lambda (path) (browse-url (concat "message:" path))))
>       ("news" :follow
> (lambda (path) (browse-url (concat "news:" path))))
>       ("shell" :follow org--open-shell-link))
>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>  )
>
>