Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

Your bug report will be posted to the Org mailing list.
So it seems that the numbering of numbered items in a plain list are not
maintained when the numbered item is also a TODO plain list item.

Here is how I produced the issue:

$ emacs -Q

I created a very simple org-mode file:
--8<---------------cut here---------------start------------->8---
* Test file
  1. [ ] item
  2. item 2
  3. item 3
--8<---------------cut here---------------end--------------->8---

I then used the export facilities to create a PDF: C-c C-e l o

I expected to see a PDF that looked like:
--8<---------------cut here---------------start------------->8---

1 Test File

1  Test File
   1. [] item
   2. item 2
   3. item 3
--8<---------------cut here---------------end--------------->8---

Instead I see a pdf that has the following:
--8<---------------cut here---------------start------------->8---

1 Test File

1  Test File
   [] item
   1. item 2
   2. item 3
--8<---------------cut here---------------end--------------->8---

Notice how the "1." was removed in the generated PDF from the first item
and the numbering started from 1. on "item 2"

This used to work, but I'm not exactly certain when it changed.

It *appears* that the generated \item for enumeration is incorrect?
The .tex file contains the following:
     \item[{$\square$}] item

I /think/ that this should be:
   \item{$\square$} item

Maybe the [ and ] are not being stripped and converted into the {$\square$}, 
but are rather being left and ending up
with [{$\square$}].

(The same thing happens with the \boxtimes for "completed" TODOs.

If that is the case then I /think/ that this patch would fix it:
diff --git a/lisp/ox-latex.el b/lisp/ox-latex.el
index 832d9bf8..b9734443 100644
--- a/lisp/ox-latex.el
+++ b/lisp/ox-latex.el
@@ -2208,9 +2208,9 @@ contextual information."
             ((and checkbox tag)
-             (format "[{%s %s}] %s" checkbox tag tag-footnotes))
+             (format "{%s %s} %s" checkbox tag tag-footnotes))
             ((or checkbox tag)
-             (format "[{%s}] %s" (or checkbox tag) tag-footnotes))
+             (format "{%s} %s" (or checkbox tag) tag-footnotes))
             ;; Without a tag or a check-box, if CONTENTS starts with
             ;; an opening square bracket, add "\relax" to "\item",
             ;; unless the brackets comes from an initial export

I haven't done any thorough testing, just looking where I thought the issue 
might be.

Thanks for all the great work on Org Mode,

Emacs  : GNU Emacs 27.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.18.9)
 of 2019-09-04
Package: Org mode version 9.1.9 (release_9.1.9-65-g5e4542 @ 

current state:
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-mode-hook '(#[0 "\300\301\302\303\304$\207"
                   [add-hook change-major-mode-hook org-show-block-all append
                 #[0 "\300\301\302\303\304$\207"
                   [add-hook change-major-mode-hook org-babel-show-result-all
                    append local]
                 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn 
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
 org-babel-pre-tangle-hook '(save-buffer)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
 org-ascii-format-drawer-function #[771 "\207" [] 4 "\n\n(fn NAME CONTENTS 
 org-occur-hook '(org-first-headline-recenter)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
 org-speed-command-hook '(org-speed-command-activate
 org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 org-link-parameters '(("id" :follow org-id-open)
                       ("rmail" :follow org-rmail-open :store
                       ("mhe" :follow org-mhe-open :store org-mhe-store-link)
                       ("irc" :follow org-irc-visit :store org-irc-store-link)
                       ("info" :follow org-info-open :export org-info-export
                        :store org-info-store-link)
                       ("gnus" :follow org-gnus-open :store
                       ("docview" :follow org-docview-open :export
                        org-docview-export :store org-docview-store-link)
                       ("bibtex" :follow org-bibtex-open :store
                       ("bbdb" :follow org-bbdb-open :export org-bbdb-export
                        :complete org-bbdb-complete-link :store
                       ("w3m" :store org-w3m-store-link) ("file+sys")
                       ("file+emacs") ("doi" :follow org--open-doi-link)
                       ("elisp" :follow org--open-elisp-link)
                       ("file" :complete org-file-complete-link)
                       ("ftp" :follow
                        (lambda (path) (browse-url (concat "ftp:" path))))
                       ("help" :follow org--open-help-link)
                       ("http" :follow
                        (lambda (path) (browse-url (concat "http:" path))))
                       ("https" :follow
                        (lambda (path) (browse-url (concat "https:" path))))
                       ("mailto" :follow
                        (lambda (path) (browse-url (concat "mailto:"; path))))
                       ("news" :follow
                        (lambda (path) (browse-url (concat "news:"; path))))
                       ("shell" :follow org--open-shell-link))
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-html-format-headline-function 'org-html-format-headline-default-function

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