Please keep in mind that the more custom fields you have on a page, the more queries it will create. As a workaround, I suggest you split the fields so WordPress doesn’t need to process a lot of data. For example, you can create a new custom post type to hold certain fields, and then use the post object field to create the relation.
It’s also possible that there’s another plugin that generates the extra queries. Could you please try to reproduce the issue on one of the WordPress’ stock themes (like Twenty Sixteen) with only ACF activated? If it disappears, then you can activate the theme and plugins one by one to see which one causes the issue.
Regarding the Local JSON feature, it should create the files as many as your field groups. Could you please clear the folder and then re-save your field groups one by one?
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