And here is the steps to reproduce this issue:

my config:

(require 'org-num)
(setq org-num-skip-footnotes t)
(add-hook 'org-mode-hook #'org-num-mode)

1. Then open an Org file, it has `org-num-mode` enabled because upper
   config added to hook.

2. Execute command with `[M-x org-mode]` again, then it will become as
   in screenshot.

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