I have a function to save the currently clocked item into a file so I
can display it in my terminal.  The hook seems to interfere with
org-capture.  If I capture something the following
happens:

1. org-capture dialog appears
2. Fill-in capture.  The capture is clocked-in.
3. Finish capture with C-c C-c
4. The capture is still clocked in.  The clock should go back to the
previous clocked-in entry.

Trying to bisect the issue was difficult.  Sometimes the new capture would
clock-out, but the original entry would not clock back in.  Other times
the clock would be left running in the new capture entry.

The smallest example I could get is:

    (defun my:org-get-clocked-in-headline ()
      "Get the headline of the currently clocked in headline.
    If no headline is clocked in, then return an empty string."
      (interactive)
      (with-current-buffer (marker-buffer org-clock-marker)
        (goto-char org-clock-marker)))

    (defun my:org-save-clocked-in-entry-to-file ()
      "Save currently clocked-in task to a file."
      (with-temp-buffer
        (insert (my:org-get-clocked-in-headline))))

    (add-hook 'org-clock-in-hook #'my:org-save-clocked-in-entry-to-file)

For reference, here's the full code I'm using

    (defun my:org-get-clocked-in-headline ()
      "Get the headline of the currently clocked in headline.
    If no headline is clocked in, then return an empty string."
      (interactive)
      (if (not (org-clocking-p))
          ""
        (with-current-buffer (marker-buffer org-clock-marker)
          (save-excursion
            (save-restriction
              (when (or (< org-clock-marker (point-min)) (>
org-clock-marker (point-max)))
                (widen))
              (goto-char org-clock-marker)
              (org-no-properties (org-get-heading 'no-tags 'no-todo)))))))

    (defvar my:org-clocked-in-file-path "/tmp/org-currently-clocked-in-task"
      "Where to save the currently clocked in task for all to see.")

    (defun my:org-save-clocked-in-entry-to-file ()
      "Save currently clocked-in task to a file."
      (let ((last-message (current-message))
            ;; Suppress echo area to see clock out information.  Doesn't
seem to
            ;; work, so we'll just re-display last-message.
            (inhibit-message nil))
        (with-temp-buffer
          (insert (my:org-get-clocked-in-headline))
          (write-region (point-min) (point-max)
my:org-clocked-in-file-path))
        (message last-message)))

    (add-hook 'org-clock-in-hook #'my:org-save-clocked-in-entry-to-file)
    (add-hook 'org-clock-out-hook #'my:org-save-clocked-in-entry-to-file)
    (add-hook 'org-clock-cancel-hook #'my:org-save-clocked-in-entry-to-file)


Emacs  : GNU Emacs 25.1.50.2 (x86_64-pc-linux-gnu, GTK+ Version 3.18.9)
 of 2016-07-14
Package: Org-mode version 8.3.4 (8.3.4-93-g0d72c3-elpaplus @
/home/joe/.emacs.d/elpa/org-20160627/)

current state:
==============
(setq
 org-id-locations-file "/home/joe/.emacs.d/.cache/.org-id-locations"
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
 org-drill-sm5-initial-interval 1.5
 org-clock-persist-file "/home/joe/.emacs.d/.cache/org-clock-save.el"
 org-habit-preceding-days 10
 org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
 org-reverse-note-order t
 org-clock-history-length 23
 org-occur-hook '(org-first-headline-recenter)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-html-format-drawer-function '(lambda (name contents) contents)
 org-capture-after-finalize-hook '(org-save-all-org-buffers)
 org-log-done t
 org-latex-format-inlinetask-function
'org-latex-format-inlinetask-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-link-translation-function 'toc-org-unhrefify
 org-present-mode-hook '(spacemacs//org-present-start)
 org-agenda-restore-windows-after-quit t
 org-latex-format-headline-function
'org-latex-format-headline-default-function
 org-default-notes-file "~/gdrive/org/refile.org"
 org-clock-in-resume t
 org-clock-cancel-hook '(my:org-save-clocked-in-entry-to-file)
 org-capture-templates '(("t" "todo" entry (file "~/gdrive/org/refile.org")
"* TODO %?\n%U\n%(my:org-pick-smart-context \"%x\")\n"
                          :clock-in t :clock-resume t)
                         ("r" "respond" entry (file "~/gdrive/org/refile.org
")
                          "* NEXT Respond to %:from on
%:subject\nSCHEDULED: %t\n%U\n%a\n" :clock-in t :clock-resume t
:immediate-finish t)
                         ("n" "note" entry (file "~/gdrive/org/refile.org")
"* %? :NOTE:\n%U\n%a\n" :clock-in t :clock-resume t)
                         ("j" "Journal" entry (file+datetree "~/gdrive/org/
journal.org") "* %?\n%U\n" :clock-in t :clock-resume t)
                         ("w" "org-protocol" entry (file "~/gdrive/org/
refile.org") "* TODO Review %c\n%U\n" :immediate-finish t)
                         ("m" "Meeting" entry (file "~/gdrive/org/refile.org")
"* MEETING with %? :MEETING:\n%U" :clock-in t :clock-resume
                          t)
                         ("p" "Phone call" entry (file "~/gdrive/org/
refile.org") "* PHONE %? :PHONE:\n%U" :clock-in t :clock-resume t)
                         ("h" "Habit" entry (file "~/gdrive/org/refile.org")
                          "* NEXT %?\n%U\n%a\nSCHEDULED:
%(format-time-string \"%<<%Y-%m-%d %a .+1d/3d>>\")\n:PROPERTIES:\n:STYLE:
habit\n:REPEAT_TO_STATE: NEXT\n:END:\n")
                         )
 org-startup-indented t
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-latex-format-drawer-function '(lambda (name contents) contents)
 org-drill-learn-fraction 0.3
 org-from-is-user-regexp "\\<joe\\>"
 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-font-lock-set-keywords-hook '(org-drill-add-cloze-fontification)
 org-mode-hook '(spacemacs/load-yasnippet toc-org-enable org-bullets-mode
org-autolist-mode org-clock-load
                 #[nil "\300\301\302\303\304$\207" [org-add-hook
change-major-mode-hook org-show-block-all append local] 5]
                 #[nil "\300\301\302\303\304$\207" [org-add-hook
change-major-mode-hook org-babel-show-result-all append local] 5]
                 org-babel-result-hide-spec org-babel-hide-all-hashes
spacemacs/add-org-surrounds evil-org-mode org-eldoc-load
                 spacemacs//init-company-org-mode company-mode)
 org-refile-targets '((nil :maxlevel . 9) (org-agenda-files :maxlevel . 9))
 org-outline-path-complete-in-steps nil
 org-todo-state-tags-triggers '(("CANCELLED" ("cancelled" . t)) ("WAITING"
("waiting" . t)) ("HOLD" ("waiting") ("hold" . t))
                                (done ("waiting") ("hold")) ("TODO"
("waiting") ("cancelled") ("hold"))
                                ("NEXT" ("waiting") ("cancelled") ("hold"))
("DONE" ("waiting") ("cancelled") ("hold")))
 org-stuck-projects '("" nil nil "")
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-agenda-compact-blocks t
 org-ascii-format-drawer-function '(lambda (name contents width) contents)
 org-clock-persist t
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
 org-refile-use-outline-path t
 org-clock-in-switch-to-state 'bh/clock-in-to-next
 org-directory "~/gdrive/org"
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
org-cycle-show-empty-lines
                  org-optimize-window-after-visibility-change)
 org-present-mode-quit-hook '(spacemacs//org-present-end)
 org-export-async-init-file
"/home/joe/.emacs.d/layers/org/org-async-init.el"
 org-clock-persist-query-resume nil
 org-todo-keywords '((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d)") (sequence
"WAITING(w@/!)" "HOLD(h@/!)" "|" "CANCELLED(c)"))
 org-modules '(org-bbdb org-bibtex org-docview org-gnus org-habit org-info
org-irc org-mhe org-rmail org-w3m org-drill)
 org-clock-report-include-clocking-task t
 org-download-image-dir "~/gdrive/org/images"
 org-confirm-elisp-link-function 'yes-or-no-p
 org-startup-with-inline-images t
 org-edit-src-content-indentation 0
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-treat-S-cursor-todo-selection-as-state-change nil
 org-html-format-headline-function
'org-html-format-headline-default-function
 org-clock-in-hook '(my:org-save-clocked-in-entry-to-file)
 org-html-format-inlinetask-function
'org-html-format-inlinetask-default-function
 org-agenda-mode-hook '(org-save-all-org-buffers)
 org-fontify-whole-heading-line t
 org-agenda-files '("~/gdrive/org/")
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer
bh/clock-out-maybe my:remove-empty-drawer-on-clock-out
                      my:org-save-clocked-in-entry-to-file)
 org-drill-add-random-noise-to-intervals-p t
 org-clock-out-remove-zero-time-clocks t
 org-publish-project-alist '(("swift-plaques" :author "Joe Schafer"
:base-directory "~/prog/swift-plaques-business-plan"
                              :publishing-directory
"~/prog/swift-plaques-business-plan" :publishing-function
org-latex-publish-to-pdf
                              :base-extension "org")
                             )
 org-tag-alist '((:startgroup) ("work" . 119) ("home" . 104) ("comp" . 99)
("errand" . 101) (:endgroup) (:startgroup) ("start" . 115)
                 ("mid" . 109) ("end" . 110) (:endgroup) (:startgroup)
("daily" . 100) ("weekly" . 107) (:endgroup) (:startgroup)
                 ("waiting" . 116) ("hold" . 104) ("cancelled" . 99)
(:endgroup))
 )