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When adding a custom sequence of todo keywords to org-todo-keywords, “[ ] -> [X]”, the function org-todo-list will not filter to those entries with keyword [ ], and entries with keyword [X] will not be displayed at all.

Steps to reproduce:

1. Add the sequence (sequence "[ ]" "[X]") to the org-todo-keywords list.

2. Add an org file with the following contents as entries to the front of the agenda list:

   [ ] Unchecked and will appear in agenda
   [X] Checked and will not appear in agenda
   TODO Todo and will appear in agenda
   DONE Done and will appear in agenda
   

   (due to a quirk of my email client, I cannot paste the above as actual entries. Their structure does not matter, so long as they are all entries.)

3. Call org-todo-list

   You will note that “Todo and will appear in agenda”, “Done and will appear in agenda”, and “Unchecked and will appear in agenda” are listed. However, “Checked and will not appear in agenda will not”.

4. Press NUM r, where NUM is the number corresponding to the keyword [ ]

   No entries will be displayed.

5. Press NUM2 r, where NUM2 is the number corresponding to the keyword [X]

   No entries will be displayed.

Despite what my org mode version says, I have tested this on the latest commit available for Emacs 28.1.

Emacs : GNU Emacs 28.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, cairo version 1.16.0) of 2022-05-31 Package: Org mode version 9.7 (9.7-??-6eb773053 @ home/shortcut.emacs.d/.local/straight/build-28.1/org/)