Just out of curiosity, does the shortcode get inserted into the standard WP editor (classic editor) instead of the ACF WYSIWYG?
I don’t really have an answer and this is only guessing. A lot of tools used for inserting content do not work correctly when there are multiple tinyMCE editors on the page and they assume that only that only the default editor exists.
I have run into this issue in the past with some plugins.
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