Explain the problem.
Activating language shorthands via babeloptions crashes LaTeX rendering.

1. Set yaml preamble of a markdown document like this

---
lang : fr
papersize : a4
babeloptions:
- shorthands=:;!?

...

2. Render document in PDF leads to this error

! Package babel Error: Bad option 'shorthands=:;!?'. Either you have misspelled
 the
(babel)                key or there is a previous setting of 'shorthands'. Vali
d
(babel)                keys are, among others, 'shorthands', 'main', 'bidi',
(babel)                'strings', 'config', 'headfoot', 'safe', 'math'..

See the babel package documentation for explanation.

Indeed Pandoc calls babel like this

\ifLuaTeX
\usepackage[bidi=basic,shorthands=off,shorthands=:;!?]{babel}
\else
\usepackage[bidi=default,shorthands=off,shorthands=:;!?]{babel}
\fi

babel doesn't allow using the shorthands key twice

Some time ago Pandoc (version 3.5) was redefining \languageshorthands to deactivate shorthands. This was reversible at the document level. Forcing shorthands=off in babel options is not. So it's also a functional regression.

There might be some reasons to deactivate shorthands by default but we should be able to activate them again.

Pandoc version?
pandoc 3.8 on Ubuntu