Hello, I think I've found some bugs with indentation of org mode
source code blocks.

Bug 1

When edited within the Org buffer, e.g. not by entering indirect
buffer with C-c ' the indentation misses two spaces (█ represents the
point):

#+begin_src emacs-lisp
  (progn 1
         2█
         3)
#+end_src

Pressing RET here results in the following indent:

#+begin_src emacs-lisp
  (progn 1
         2
       █
         3)
#+end_src

But inputting a number and pressing TAB will indent it correctly:

#+begin_src emacs-lisp
  (progn 1
         2
         0█
         3)
#+end_src

Org doesn't seem to take into account the leading two space
indentation, and sends deindented buffer to indent function.

(See demo-1.mp4 for more clear view of the problem)

Bug 2

Org mode adds extra two space indent to whole expression if point is
before the closing parenthesis:

#+begin_src emacs-lisp
  (progn 1
         2
         3█)
#+end_src

Pressing RET here produces extra indentation:

#+begin_src emacs-lisp
    (progn 1
           2
           3
           █)
#+end_src

(See demo-2.mp4 for more clear view of the problem)

All of this occurs in emacs -q with GNU Emacs 28.0.50.

Now, I must say, that setting `org-src-preserve-indentation' variable
to `t' "fixes" the issue.  Org will correctly indent code, but will
preserve these additional spaces when entering indirect buffer.  I
like the default behavior more, e.g. having two spaces before the code
in Org buffer, and not having these spaces in indirrect buffer.  It
seems to me that the fix would be to let bind this variable to `t' ony
when indenting the code, but there might be a better solution.
Currenlty I've have this workaround in my config:

(define-advice org-return (:around (f &optional indent arg
interactive) aorst:org-return)
  (let ((org-src-preserve-indentation t))
    (funcall f indent arg interactive)))
(define-advice org-cycle (:around (f &optional arg) aorst:org-cycle)
  (let ((org-src-preserve-indentation t))
    (funcall f arg)))

Though this fixes the error, I think it is a hack.

Emacs  : GNU Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version
3.24.13, cairo version 1.16.0)
 of 2021-01-17
Package: Org mode version 9.4.4 (release_9.4.4 @
/home/andreyorst/.local/emacs/share/emacs/28.0.50/lisp/org/)

current state:
==============
(setq
 org-confirm-elisp-link-function 'yes-or-no-p
 org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
 org-occur-hook '(org-first-headline-recenter)
 org-babel-pre-tangle-hook '(save-buffer)
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-hide-drawers org-cycle-show-empty-lines
          org-optimize-window-after-visibility-change)
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-agenda-loop-over-headlines-in-active-region nil
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-confirm-shell-link-function 'yes-or-no-p
 org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
"\n\n(fn ENTRY)"]
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-mode-hook '(#[0 "\300\301\302\303\304$\207" [add-hook
change-major-mode-hook org-show-all append local] 5]
         #[0 "\300\301\302\303\304$\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-metaup-hook '(org-babel-load-in-session-maybe)
 org-link-shell-confirm-function 'yes-or-no-p
 org-link-parameters '(("attachment" :follow org-attach-follow
:complete org-attach-complete-link)
               ("id" :follow org-id-open) ("eww" :follow org-eww-open
:store org-eww-store-link)
               ("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
:export org-irc-export)
               ("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")
               ("shell" :follow org-link--open-shell)
               ("news" :follow
            #[514 "\301\300\302 Q \"\207" ["news" browse-url ":"] 6
"\n\n(fn URL ARG)"])
               ("mailto" :follow
            #[514 "\301\300\302 Q \"\207" ["mailto" browse-url ":"] 6
"\n\n(fn URL ARG)"])
               ("https" :follow
            #[514 "\301\300\302 Q \"\207" ["https" browse-url ":"] 6
"\n\n(fn URL ARG)"])
               ("http" :follow
            #[514 "\301\300\302 Q \"\207" ["http" browse-url ":"] 6
"\n\n(fn URL ARG)"])
               ("ftp" :follow
            #[514 "\301\300\302 Q \"\207" ["ftp" browse-url ":"] 6
"\n\n(fn URL ARG)"])
               ("help" :follow org-link--open-help) ("file" :complete
org-link-complete-file)
               ("elisp" :follow org-link--open-elisp) ("doi" :follow
org-link--open-doi))
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-link-elisp-confirm-function 'yes-or-no-p
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 )

--
Best regards,
Andrey Listopadov