Reproduction:

1. emacs -Q
2. Enable org-mode in the scratch buffer (M-x org-mode)
3. Paste this code:

#+begin_src emacs-lisp

(with-eval-after-load 'evil
(define-key evil-insert-state-map (kbd "C-S-v") 'yank)
(define-key evil-visual-state-map (kbd "{") 'evil-backward-paragraph)
(define-key evil-visual-state-map (kbd "}") 'evil-forward-paragraph)
(define-key evil-insert-state-map (kbd "M-w") 'evil-forward-word-begin)
(define-key evil-insert-state-map (kbd "M-b") 'evil-backward-word-begin)
(define-key evil-insert-state-map (kbd "M-W") 'evil-forward-WORD-begin)
(define-key evil-insert-state-map (kbd "M-B") 'evil-backward-WORD-begin)

(define-key evil-normal-state-map (kbd "gq") 'FormatToThreshold)
(define-key evil-visual-state-map (kbd "gq") 'FormatToThreshold))

(defun my-move-beginning-of-line ()
"Move point to the first non-whitespace character of the line and enter insert mode."
(interactive)
(evil-first-non-blank)
(evil-insert-state))

#+end_src

(with-eval-after-load 'evil
(define-key evil-insert-state-map (kbd "C-S-v") 'yank)
(define-key evil-visual-state-map (kbd "{") 'evil-backward-paragraph)
(define-key evil-visual-state-map (kbd "}") 'evil-forward-paragraph)
(define-key evil-insert-state-map (kbd "M-w") 'evil-forward-word-begin)
(define-key evil-insert-state-map (kbd "M-b") 'evil-backward-word-begin)
(define-key evil-insert-state-map (kbd "M-W") 'evil-forward-WORD-begin)
(define-key evil-insert-state-map (kbd "M-B") 'evil-backward-WORD-begin)

(define-key evil-normal-state-map (kbd "gq") 'FormatToThreshold)
(define-key evil-visual-state-map (kbd "gq") 'FormatToThreshold))

(defun my-move-beginning-of-line ()
"Move point to the first non-whitespace character of the line and enter insert mode."
(interactive)
(evil-first-non-blank)
(evil-insert-state))

4. Highlight the first code paragrapth in the org code block:

(with-eval-after-load 'evil
(define-key evil-insert-state-map (kbd "C-S-v") 'yank)
(define-key evil-visual-state-map (kbd "{") 'evil-backward-paragraph)
(define-key evil-visual-state-map (kbd "}") 'evil-forward-paragraph)
(define-key evil-insert-state-map (kbd "M-w") 'evil-forward-word-begin)
(define-key evil-insert-state-map (kbd "M-b") 'evil-backward-word-begin)
(define-key evil-insert-state-map (kbd "M-W") 'evil-forward-WORD-begin)
(define-key evil-insert-state-map (kbd "M-B") 'evil-backward-WORD-begin)

5. Execute 'comment-region'. It will apply partial commenting on the
next line like this:

;; (with-eval-after-load 'evil
;; (define-key evil-insert-state-map (kbd "C-S-v") 'yank)
;; (define-key evil-visual-state-map (kbd "{") 'evil-backward-paragraph)
;; (define-key evil-visual-state-map (kbd "}") 'evil-forward-paragraph)
;; (define-key evil-insert-state-map (kbd "M-w") 'evil-forward-word-begin)
;; (define-key evil-insert-state-map (kbd "M-b") 'evil-backward-word-begin)
;; (define-key evil-insert-state-map (kbd "M-W") 'evil-forward-WORD-begin)
;; (define-key evil-insert-state-map (kbd "M-B") 'evil-backward-WORD-begin)

;; (define-key e
vil-normal-state-map (kbd "gq") 'FormatToThreshold)

6. Now apply highlighting and comment the same code, but outside of the
org code block, and the end result will be correct:

# (with-eval-after-load 'evil
# (define-key evil-insert-state-map (kbd "C-S-v") 'yank)
# (define-key evil-visual-state-map (kbd "{") 'evil-backward-paragraph)
# (define-key evil-visual-state-map (kbd "}") 'evil-forward-paragraph)
# (define-key evil-insert-state-map (kbd "M-w") 'evil-forward-word-begin)
# (define-key evil-insert-state-map (kbd "M-b") 'evil-backward-word-begin)
# (define-key evil-insert-state-map (kbd "M-W") 'evil-forward-WORD-begin)
# (define-key evil-insert-state-map (kbd "M-B") 'evil-backward-WORD-begin)

Emacs : GNU Emacs 30.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.41, cairo version 1.18.0)
of 2024-04-23
Package: Org mode version 9.8-pre (release_9.7.6-101-g4f6aab @ /home/wurfkreuz/.emacs.d/straight/build/org/)